Aeropyrum pernix (DSM 11879, JCM 9820, K1)

Name: Aeropyrum pernix (DSM 11879, JCM 9820, K1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 4195

Type strain

Strain Designation K1

Culture col. no. DSM 11879 JCM 9820 K1 ATCC 700893 NBRC 100138

NCBI tax ID(s) 56636

Special Collections DSMZ JCM Literature strains

History DSMZ <- JCM; JCM 9820 <- N. Nomura, Kyoto Univ., Japan; K1 JCM <-- N. Nomura K1.

Links

Aeropyrum pernix K1 is an aerobe, heterotroph, Gram-negative archaeon that forms irregular colonies and was isolated from marine solfataric vent.

Gram-negative motile coccus-shaped colony-forming aerobe heterotroph genome sequence 16S sequence Archaea

Name and taxonomic classification

SI-ID 44195

ATCC 700893,JCM 9820,DSM 11879,NBRC 100138

@ref 20215

Last LPSN update 2026-05-29 08:25:52

Domain Archaea

Phylum Thermoproteota

Class Thermoprotei

Order Acidilobales

Family Acidilobaceae

Genus Aeropyrum

Species Aeropyrum pernix

Full scientific name Aeropyrum pernix Sako et al. 1996

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell shape	Motility
23222	negative	0.8-1.0 µm	coccus-shaped

Colony morphology

@ref	Colony color	Colony shape
23222	brown	irregular

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
4521	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l Na2S2O3 x 5 H2O 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
4521	positive	growth	90
23222	positive	growth	70-100
23222	negative	growth	68
23222	negative	growth	102
23222	positive	optimum	90-95
67770	positive	growth	90

Culture pH

@ref	Ability	Type	PH	PH range
23222	positive	optimum	7.0
23222	positive	growth	5-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
23222	aerobe
125439	anaerobe	98.849

Nutrition type

23222

Typeheterotroph

Spore formation

@ref	Spore formation	Confidence
125438		91.512

Observation

67770

Observationquinones: DMK-6(H_n), MTK-6(H_n)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23222	16094 ChEBI	thiosulfate	+	growth

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Condition	#Sulfuric	-
#Condition	#Thermophilic (>45°C)	-
#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Volcanic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
4521	marine solfataric vent	Kodakara-Jima Island	Japan	JPN	Asia
23222	hot sedimentary materials and venting waters at a coastal solfataric vent
67770	Coastal solfataric vent at Kodakara-Jima Island		Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4521	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1112v1 assembly for Aeropyrum pernix K1	complete	GCA_000011125	272557.25	2923402010	272557	96.94

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
4521	Aeropyrum pernix gene for 16S rRNA, partial sequence	D83259	1444		56636
67770	Aeropyrum pernix genes for 16S rRNA, 23S rRNA and rRNA intron-encoded homing endonuclease, complete cds	AB008745	10777		56636

GC content

@ref	GC-content (mol%)	Method
4521	67	high performance liquid chromatography (HPLC)
23222	67.0	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1112v1 assembly for Aeropyrum pernix K1
BV-BRC: 272557.25

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	98.85	no
125439	gram_stain	BacteriaNetⓘ	positive	49.79	no
125439	motility	BacteriaNetⓘ	no	61.21	no
125439	spore_formation	BacteriaNetⓘ	yes	55.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Aeropyrum pernix K1 K1
NCBI: GCA_000011125.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	78.25	yes
125438	anaerobic	anaerobicⓘ	yes	50.35	yes
125438	aerobic	aerobicⓘ	no	56.33	no
125438	spore-forming	spore-formingⓘ	no	91.51	no
125438	thermophilic	thermophileⓘ	yes	82.40	yes
125438	flagellated	motile2+ⓘ	no	84.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Chromosome architecture in an archaeal species naturally lacking structural maintenance of chromosomes proteins.	Badel C, Bell SD.	Nat Microbiol	10.1038/s41564-023-01540-6	2024
	The evolution of archaeal flagellar filaments.	Kreutzberger MAB, Cvirkaite-Krupovic V, Liu Y, Baquero DP, Liu J, Sonani RR, Calladine CR, Wang F, Krupovic M, Egelman EH.	Proc Natl Acad Sci U S A	10.1073/pnas.2304256120	2023
Genetics	Cell cycle characteristics of crenarchaeota: unity among diversity.	Lundgren M, Malandrin L, Eriksson S, Huber H, Bernander R.	J Bacteriol	10.1128/jb.00330-08	2008
Metabolism	The first archaeal ATP-dependent glucokinase, from the hyperthermophilic crenarchaeon Aeropyrum pernix, represents a monomeric, extremely thermophilic ROK glucokinase with broad hexose specificity.	Hansen T, Reichstein B, Schmid R, Schonheit P.	J Bacteriol	10.1128/jb.184.21.5955-5965.2002	2002
Enzymology	Comprehensive mutagenesis to identify amino acid residues contributing to the difference in thermostability between two originally thermostable ancestral proteins.	Akanuma S, Yamaguchi M, Yamagishi A.	PLoS One	10.1371/journal.pone.0258821	2021
Metabolism	Structural and functional insights into Aeropyrum pernix OppA, a member of a novel archaeal OppA subfamily.	Balestrieri M, Gogliettino M, Fiume I, Pocsfalvi G, Catara G, Rossi M, Palmieri G.	J Bacteriol	10.1128/jb.00899-10	2011
Metabolism	Enzymatic degradation of PrPSc by a protease secreted from Aeropyrum pernix K1.	Snajder M, Vilfan T, Cernilec M, Rupreht R, Popovic M, Juntes P, Serbec VC, Ulrih NP.	PLoS One	10.1371/journal.pone.0039548	2012
Stress	Inhibitory effect of Maillard reaction products on growth of the aerobic marine hyperthermophilic archaeon Aeropyrum pernix.	Kim KW, Lee SB.	Appl Environ Microbiol	10.1128/aem.69.7.4325-4328.2003	2003
Metabolism	Outside the unusual cell wall of the hyperthermophilic archaeon Aeropyrum pernix K1.	Palmieri G, Cannio R, Fiume I, Rossi M, Pocsfalvi G.	Mol Cell Proteomics	10.1074/mcp.m900012-mcp200	2009
Genetics	Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate.	Rodionov DA, Kurnasov OV, Stec B, Wang Y, Roberts MF, Osterman AL.	Proc Natl Acad Sci U S A	10.1073/pnas.0609279104	2007
Enzymology	Highly stable L-lysine 6-dehydrogenase from the thermophile Geobacillus stearothermophilus isolated from a Japanese hot spring: characterization, gene cloning and sequencing, and expression.	Heydari M, Ohshima T, Nunoura-Kominato N, Sakuraba H.	Appl Environ Microbiol	10.1128/aem.70.2.937-942.2004	2004
	Large-Scale Molecular Evolutionary Analysis Uncovers a Variety of Polynucleotide Kinase Clp1 Family Proteins in the Three Domains of Life.	Saito M, Sato A, Nagata S, Tamaki S, Tomita M, Suzuki H, Kanai A.	Genome Biol Evol	10.1093/gbe/evz195	2019
Metabolism	Induced fit and the catalytic mechanism of isocitrate dehydrogenase.	Goncalves S, Miller SP, Carrondo MA, Dean AM, Matias PM.	Biochemistry	10.1021/bi300483w	2012
	Molecular dynamics simulations at high temperatures of the Aeropyrum pernix L7Ae thermostable protein: Insight into the unfolding pathway.	Benrezkallah D.	J Mol Graph Model	10.1016/j.jmgm.2023.108700	2024
Lipids	Effects of producing high levels of hyperthermophile-specific C₂₅,C₂₅-archaeal membrane lipids in Escherichia coli.	Yoshida R, Motoyama K, Ito T, Hemmi H.	Biochem Biophys Res Commun	10.1016/j.bbrc.2024.150349	2024
Genetics	X-ray crystal structure of proliferating cell nuclear antigen 1 from Aeropyrum pernix.	Yamauchi T, Kikuchi M, Iizuka Y, Tsunoda M.	Acta Crystallogr F Struct Biol Commun	10.1107/s2053230x24009518	2024
	Self-assembly of Aeropyrum pernix bacilliform virus 1 (APBV1) major capsid protein and its application as building blocks for nanomaterials.	Sumikama Y, Takashima A, Mochizuki T, Sakuraba H, Ohshima T, Sugihara S, Suye SI, Satomura T.	Extremophiles	10.1007/s00792-022-01284-x	2022
Enzymology	Bioprocess development to produce a hyperthermostable S-methyl-5'-thioadenosine phosphorylase in Escherichia coli.	Schollmeyer J, Waldburger S, Njo K, Yehia H, Kurreck A, Neubauer P, Riedel SL.	Biotechnol Bioeng	10.1002/bit.28526	2023
	A mutation in the S6 segment of the KvAP channel changes the secondary structure and alters ion channel activity in a lipid bilayer membrane.	Malik C, Ghosh S.	Amino Acids	10.1007/s00726-022-03188-8	2022
Genetics	Archaeal DNA replication initiation: bridging LUCA's legacy and modern mechanisms.	Dulermo R.	Front Microbiol	10.3389/fmicb.2025.1561973	2025
	Biochemical characterization and mutational analysis of a mismatch glycosylase from the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5.	Wang L, Lin T, Oger P, Gong Y, Zhang L.	DNA Repair (Amst)	10.1016/j.dnarep.2022.103321	2022
	Identification of novel components of the Ced and Ups systems in Saccharolobus islandicus REY15A.	Wu P, Zhang M, Kou Y, Liang S, Ni J, Huang Q, Shen Y.	mLife	10.1002/mlf2.12163	2025
Enzymology	Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix with ATP and AMP.	Shibanuma Y, Nemoto N, Yamamoto N, Sampei GI, Kawai G.	J Biochem	10.1093/jb/mvaa043	2020
	Total Synthesis and Structure Confirmation of trans-Anhydromevalonate-5-phosphate, a Key Biosynthetic Intermediate of the Archaeal Mevalonate Pathway.	Yasuno Y, Nakayama A, Saito K, Kitsuwa K, Okamura H, Komeyama M, Hemmi H, Shinada T.	J Nat Prod	10.1021/acs.jnatprod.1c00615	2021
	Enhanced isoprenoid production in Escherichia coli cells harboring the archaeal mevalonate pathway.	Takahashi T, Saito T, Dohgami I, Ito T, Hemmi H.	Biochem Biophys Rep	10.1016/j.bbrep.2025.102307	2025
	Modulation of Kv Channel Gating by Light-Controlled Membrane Thickness.	Yadav R, Pfeffermann J, Goessweiner-Mohr N, Glasnov T, Akimov SA, Pohl P.	Biomolecules	10.3390/biom15050744	2025
	Periplasmic production of pernisine in Escherichia coli and determinants for its high thermostability.	Bahun M, Hartman K, Poklar Ulrih N.	Appl Microbiol Biotechnol	10.1007/s00253-020-10791-w	2020
	A [4Fe-4S] cluster resides at the active center of phosphomevalonate dehydratase, a key enzyme in the archaeal modified mevalonate pathway.	Komeyama M, Kanno K, Mino H, Yasuno Y, Shinada T, Ito T, Hemmi H.	Front Microbiol	10.3389/fmicb.2023.1150353	2023
	Rebuilding Ring-Type Assembly of Peroxiredoxin by Chemical Modification.	Himiyama T, Tsuchiya Y, Yonezawa Y, Nakamura T.	Bioconjug Chem	10.1021/acs.bioconjchem.0c00587	2021
	Mining unique cysteine synthetases and computational study on thoroughly eliminating feedback inhibition through tunnel engineering.	Xu S, Li ZL, Li ZM, Liu HL.	Protein Sci	10.1002/pro.5160	2024
Enzymology	Thermostable Enzyme Variants in the Lower Mevalonate Pathway Improve Isoprenoid Production by Cell-Free Biocatalysis.	Sarnik SA, Martinsen MR, Korman TP, Schwartz DK, Kaar JL, Bomble YJ.	ACS Sustain Chem Eng	10.1021/acssuschemeng.5c03763	2025
	Ligand binding Pro-miscuity of acylpeptide hydrolase, structural analysis of a detoxifying serine hydrolase.	Kiss-Szeman AJ, Takacs L, Jakli I, Banoczi Z, Hosogi N, Traore DAK, Harmat V, Perczel A, Menyhard DK.	Protein Sci	10.1002/pro.70320	2025
Metabolism	A L-proline/O₂ biofuel cell using L-proline dehydrogenase (LPDH) from Aeropyrum pernix.	Tonooka A, Komatsu T, Tanaka S, Sakamoto H, Satomura T, Suye SI.	Mol Biol Rep	10.1007/s11033-018-4328-z	2018
	Enhanced Site-Specific Fluorescent Labeling of Membrane Proteins Using Native Nanodiscs.	Ezsias B, Wolkenstein F, Goessweiner-Mohr N, Yadav R, Siligan C, Posch S, Horner A, Vargas C, Keller S, Pohl P.	Biomolecules	10.3390/biom15020254	2025
	Antioxidative Activity of Methanolic and Water Extracts from the Hyperthermophilic Archaeon Aeropyrum pernix K1.	Skrt M, Jamnik P, Poklar Ulrih N.	Acta Chim Slov	10.17344/acsi.2017.3765	2018
	Stereospecific Enzymatic Conversion of Boronic Acids to Amines.	Hanley D, Li ZQ, Gao S, Virgil SC, Arnold FH, Alfonzo E.	J Am Chem Soc	10.1021/jacs.4c04190	2024
	MicroED Structure of a Protoglobin Reactive Carbene Intermediate.	Danelius E, Porter NJ, Unge J, Arnold FH, Gonen T.	J Am Chem Soc	10.1021/jacs.2c12004	2023
Enzymology	Identification of six important amino acid residues of MenA from Bacillus subtilis natto for enzyme activity and formation of menaquinone.	Hu LX, Feng JJ, Wu J, Li W, Gningue SM, Yang ZM, Wang Z, Liu Y, Xue ZL.	Enzyme Microb Technol	10.1016/j.enzmictec.2020.109583	2020
	Biocatalytic Carbene Transfer Using Diazirines.	Porter NJ, Danelius E, Gonen T, Arnold FH.	J Am Chem Soc	10.1021/jacs.2c02723	2022
Metabolism	Biosynthetic machinery for C₂₅,C₂₅-diether archaeal lipids from the hyperthermophilic archaeon Aeropyrum pernix.	Yoshida R, Yoshimura T, Hemmi H.	Biochem Biophys Res Commun	10.1016/j.bbrc.2018.02.028	2018
Metabolism	NanoRNase from Aeropyrum pernix shows nuclease activity on ssDNA and ssRNA.	Deng YJ, Feng L, Zhou H, Xiao X, Wang FP, Liu XP.	DNA Repair (Amst)	10.1016/j.dnarep.2018.03.005	2018
Genetics	Archaeal Orc1 protein interacts with T-rich single-stranded DNA.	Wegrzyn K, Konieczny I.	BMC Res Notes	10.1186/s13104-021-05690-w	2021
	Recombinant Expression of Archaeal Superoxide Dismutases in Plant Cell Cultures: A Sustainable Solution with Potential Application in the Food Industry.	Gogliettino M, Arciello S, Cillo F, Carluccio AV, Palmieri G, Apone F, Ambrosio RL, Anastasio A, Gratino L, Carola A, Cocca E.	Antioxidants (Basel)	10.3390/antiox11091731	2022
	An enzyme-centric approach for constructing an amperometric l-malate biosensor with a long and programmable linear range.	Matthews CJ, Patrick WM.	Protein Sci	10.1002/pro.4743	2023
	Production of the Sesquiterpene Bisabolene From One- and Two-Carbon Compounds in Engineered Methanosarcina acetivorans.	Mentrup A, Scheitz LV, Wallenfang T, Rother M.	Microb Biotechnol	10.1111/1751-7915.70105	2025
Enzymology	Enzymological characteristics of a novel archaeal dye-linked D-lactate dehydrogenase showing loose binding of FAD.	Satomura T, Hayashi J, Ohshida T, Sakuraba H, Ohshima T, Suye SI.	Extremophiles	10.1007/s00792-018-1054-3	2018
	The role of tRNA identity elements in aminoacyl-tRNA editing.	Cruz E, Vargas-Rodriguez O.	Front Microbiol	10.3389/fmicb.2024.1437528	2024
	RNA Aptamers for a tRNA-Binding Protein from Aeropyrum pernix with Homologous Counterparts Distributed Throughout Evolution.	Ohmori S, Wani M, Kitabatake S, Nakatsugawa Y, Ando T, Umehara T, Tamura K.	Life (Basel)	10.3390/life10020011	2020
Phylogeny	Evolution of sequence, structural and functional diversity of the ubiquitous DNA/RNA-binding Alba domain.	Jagadeesh J, Vembar SS.	Sci Rep	10.1038/s41598-024-79937-4	2024
	Alteration of molecular assembly of peroxiredoxins from hyperthermophilic archaea.	Nakamura T, Oshima M, Yasuda M, Shimamura A, Morita J, Uegaki K.	J Biochem	10.1093/jb/mvx045	2017
	Genome mining of cryptic bisabolenes that were biosynthesized by intramembrane terpene synthases from Antrodia cinnamomea.	Hewage RT, Tseng CC, Liang SY, Lai CY, Lin HC.	Philos Trans R Soc Lond B Biol Sci	10.1098/rstb.2022.0033	2023
	Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery.	Beltran LC, Cvirkaite-Krupovic V, Miller J, Wang F, Kreutzberger MAB, Patkowski JB, Costa TRD, Schouten S, Levental I, Conticello VP, Egelman EH, Krupovic M.	Nat Commun	10.1038/s41467-023-36349-8	2023
Metabolism	Preparation of 1L-myo-Inositol 1-Phosphate as a Substrate of Phosphatidylinositol Phosphate Synthase.	Morii H, Nishimura T, Takeo M, Katayama C, Nakai K.	J UOEH	10.7888/juoeh.40.217	2018
	Kalium 3.0 is a comprehensive depository of natural, artificial, and labeled polypeptides acting on potassium channels.	Krylov NA, Tabakmakher VM, Yureva DA, Vassilevski AA, Kuzmenkov AI.	Protein Sci	10.1002/pro.4776	2023
Enzymology	The Radical SAM Heme Synthase AhbD from Methanosarcina barkeri Contains Two Auxiliary [4Fe-4S] Clusters.	Fix I, Heidinger L, Friedrich T, Layer G.	Biomolecules	10.3390/biom13081268	2023
	New components of the community-based DNA-repair mechanism in Sulfolobales.	Recalde A, Wagner A, Sivabalasarma S, Yurmashava A, Fehr NP, Thurm R, Le TN, Koebler C, Wassmer B, Albers SV, van Wolferen M.	Microlife	10.1093/femsml/uqaf002	2025
	Crystal structure of translation initiation factor 5B from the crenarchaeon Aeropyrum pernix.	Murakami R, Miyoshi T, Uchiumi T, Ito K.	Proteins	10.1002/prot.25009	2016
Metabolism	Perchlorate and chlorate reduction by the Crenarchaeon Aeropyrum pernix and two thermophilic Firmicutes.	Liebensteiner MG, Pinkse MW, Nijsse B, Verhaert PD, Tsesmetzis N, Stams AJ, Lomans BP.	Environ Microbiol Rep	10.1111/1758-2229.12335	2015
	Using several pseudo amino acid composition types and different machine learning algorithms to classify and predict archaeal phospholipases.	Samman N, Mohabatkar H, Rabiei P.	Mol Biol Res Commun	10.22099/mbrc.2023.47756.1845	2023
	A thermophilic 8-oxoguanine DNA glycosylase from Thermococcus barophilus Ch5 is a new member of AGOG DNA glycosylase family	Wang L, Jiang D, Zhang L.	Acta Biochim Biophys Sin (Shanghai)	10.3724/abbs.2022072	2022
	Heme A synthase in bacteria depends on one pair of cysteinyls for activity.	Lewin A, Hederstedt L.	Biochim Biophys Acta	10.1016/j.bbabio.2015.11.008	2016
Enzymology	Enantioselective Resolution of gamma-Lactam by a Novel Thermostable Type II (+)-gamma-Lactamase from the Hyperthermophilic Archaeon Aeropyrum pernix.	Ren L, Zhu S, Shi Y, Gao S, Zheng G.	Appl Biochem Biotechnol	10.1007/s12010-015-1565-7	2015
	Structural analysis of phosphoribosyltransferase-mediated cell wall precursor synthesis in Mycobacterium tuberculosis.	Gao S, Wu F, Gurcha SS, Batt SM, Besra GS, Rao Z, Zhang L.	Nat Microbiol	10.1038/s41564-024-01643-8	2024
Genetics	Archaea Microbiome Dysregulated Genes and Pathways as Molecular Targets for Lung Adenocarcinoma and Squamous Cell Carcinoma.	Uzelac M, Li Y, Chakladar J, Li WT, Ongkeko WM.	Int J Mol Sci	10.3390/ijms231911566	2022
Lipids	Bilayer-Forming Lipids Enhance Archaeal Monolayer Membrane Stability.	Saracco M, Schaeffer P, Tourte M, Albers SV, Louis Y, Peters J, Deme B, Fontanay S, Oger PM.	Int J Mol Sci	10.3390/ijms26073045	2025
Phylogeny	Diversity of the Tryptophanase Gene and Its Evolutionary Implications in Living Organisms.	Boya BR, Kumar P, Lee JH, Lee J.	Microorganisms	10.3390/microorganisms9102156	2021
Enzymology	Catalytically distinct states captured in a crystal lattice: the substrate-bound and scavenger states of acylaminoacyl peptidase and their implications for functionality.	Menyhard DK, Orgovan Z, Szeltner Z, Szamosi I, Harmat V.	Acta Crystallogr D Biol Crystallogr	10.1107/s1399004714026819	2015
Metabolism	Structure of the Prx6-subfamily 1-Cys peroxiredoxin from Sulfolobus islandicus.	Stroobants S, Van Molle I, Saidi Q, Jonckheere K, Maes D, Peeters E.	Acta Crystallogr F Struct Biol Commun	10.1107/s2053230x19006472	2019
Metabolism	TK2268 encodes the major aminotransferase involved in the conversion from oxaloacetic acid to aspartic acid in Thermococcus kodakarensis.	Su Y, Michimori Y, Fukuyama Y, Shimamura S, Nunoura T, Atomi H.	Appl Environ Microbiol	10.1128/aem.02017-24	2025
	Reactivity of a Recombinant Esterase from Thermus thermophilus HB27 in Aqueous and Organic Media.	Gonzalez-Gonzalez R, Fucinos P, Beneventi E, Lopez-Lopez O, Pampin B, Rodriguez R, Gonzalez-Siso MI, Cruces J, Rua ML.	Microorganisms	10.3390/microorganisms10050915	2022
	Mobility Measurements Probe Conformational Changes in Membrane Proteins due to Tension.	Morris RG, Turner MS.	Phys Rev Lett	10.1103/physrevlett.115.198101	2015
Metabolism	Structure features of Streptococcus pneumoniae FabG and virtual screening of allosteric inhibitors.	Xu K, Zhong J, Li J, Cao Y, Wei L.	Front Mol Biosci	10.3389/fmolb.2024.1472252	2024
	Archaeal mevalonate pathway in the uncultured bacterium Candidatus Promineifilum breve belonging to the phylum Chloroflexota.	Kanno K, Kuriki R, Yasuno Y, Shinada T, Ito T, Hemmi H.	Appl Environ Microbiol	10.1128/aem.01106-24	2024
Enzymology	Identification and characterization of a novel (+)-gamma-lactamase from Microbacterium hydrocarbonoxydans.	Gao S, Huang R, Zhu S, Li H, Zheng G.	Appl Microbiol Biotechnol	10.1007/s00253-016-7643-0	2016
Metabolism	Substrate specificity of undecaprenyl diphosphate synthase from the hyperthermophilic archaeon Aeropyrum pernix.	Mori T, Ogawa T, Yoshimura T, Hemmi H.	Biochem Biophys Res Commun	10.1016/j.bbrc.2013.05.081	2013
Pathogenicity	Cytotoxicity and uptake of archaeosomes prepared from Aeropyrum pernix lipids.	Napotnik TB, Valant J, Gmajner D, Passamonti S, Miklavcic D, Ulrih NP.	Hum Exp Toxicol	10.1177/0960327113477875	2013
	Insights into the Maturation of Pernisine, a Subtilisin-Like Protease from the Hyperthermophilic Archaeon Aeropyrum pernix.	Bahun M, Snajder M, Turk D, Poklar Ulrih N.	Appl Environ Microbiol	10.1128/aem.00971-20	2020
	Structural and biochemical insights into the molecular mechanism of TRPT1 for nucleic acid ADP-ribosylation.	Yang X, Wang J, Li S, Li X, Gong J, Yan Z, Zhou H, Wu C, Liu X.	Nucleic Acids Res	10.1093/nar/gkad525	2023
Proteome	Deep learning reveals antibiotics in the archaeal proteome.	Torres MDT, Wan F, de la Fuente-Nunez C.	Nat Microbiol	10.1038/s41564-025-02061-0	2025
Phylogeny	Malivhu: A Comprehensive Bioinformatics Resource for Filtering SARS and MERS Virus Proteins by Their Classification, Family and Species, and Prediction of Their Interactions Against Human Proteins.	Guevara-Barrientos D, Kaundal R.	Bioinform Biol Insights	10.1177/11779322241263671	2024
	A novel sequence-based predictor for identifying and characterizing thermophilic proteins using estimated propensity scores of dipeptides.	Charoenkwan P, Chotpatiwetchkul W, Lee VS, Nantasenamat C, Shoombuatong W.	Sci Rep	10.1038/s41598-021-03293-w	2021
	Thermoacidophilic Alicyclobacillus Superoxide Dismutase: Good Candidate as Additives in Food and Medicine.	Dong X, Wang W, Li S, Han H, Lv P, Yang C.	Front Microbiol	10.3389/fmicb.2021.577001	2021
Enzymology	Highly Efficient Multi-Step Oxidation Bioanode Using Microfluidic Channels.	Komatsu T, Hishii K, Kimura M, Amaya S, Sakamoto H, Takamura E, Satomura T, Suye SI.	Int J Mol Sci	10.3390/ijms222413503	2021
Metabolism	Modified mevalonate pathway of the archaeon Aeropyrum pernix proceeds via trans-anhydromevalonate 5-phosphate.	Hayakawa H, Motoyama K, Sobue F, Ito T, Kawaide H, Yoshimura T, Hemmi H.	Proc Natl Acad Sci U S A	10.1073/pnas.1809154115	2018
Enzymology	Two-step efficient synthesis of 5-methyluridine via two thermostable nucleoside phosphorylase from Aeropyrum pernix.	Zhu S, Ren L, Wang J, Zheng G, Tang P.	Bioorg Med Chem Lett	10.1016/j.bmcl.2011.12.142	2012
Enzymology	Studies on crenarchaeal tyrosylation accuracy with mutational analyses of tyrosyl-tRNA synthetase and tyrosine tRNA from Aeropyrum pernix.	Iwaki J, Endo K, Ichikawa T, Suzuki R, Fujimoto Z, Momma M, Kuno A, Nishimura S, Hasegawa T.	J Biochem	10.1093/jb/mvs114	2012
Genetics	Two Family B DNA Polymerases From Aeropyrum pernix, Based on Revised Translational Frames.	Daimon K, Ishino S, Imai N, Nagumo S, Yamagami T, Matsukawa H, Ishino Y.	Front Mol Biosci	10.3389/fmolb.2018.00037	2018
Metabolism	Biochemical characterization of RNase HII from Aeropyrum pernix.	Hou J, Liu Y, Lu Z, Liu X, Liu J.	Acta Biochim Biophys Sin (Shanghai)	10.1093/abbs/gms011	2012
	Donor strand complementation and calcium ion coordination drive the chaperone-free polymerization of archaeal cannulae.	Sleutel M, Sonani RR, Miller JG, Wang F, Gonzalez Socorro A, Chen Y, Martin R, Demeler B, Rudolph MJ, Alva V, Remaut H, Egelman EH, Conticello VP.	Nat Commun	10.1038/s41467-025-64120-8	2025
Enzymology	Gene expression and characterization of a third type of dye-linked L-proline dehydrogenase from the aerobic hyperthermophilic archaeon, Aeropyrum pernix.	Satomura T, Hara Y, Suye S, Sakuraba H, Ohshima T.	Biosci Biotechnol Biochem	10.1271/bbb.110775	2012
	Genome-Wide Identification of Superoxide Dismutase and Expression in Response to Fruit Development and Biological Stress in Akebia trifoliata: A Bioinformatics Study.	Yang H, Zhang Q, Zhong S, Yang H, Ren T, Chen C, Tan F, Cao G, Liu J, Luo P.	Antioxidants (Basel)	10.3390/antiox12030726	2023
Metabolism	Enhanced activity and enantioselectivity of a hyperthermophilic esterase from archaeon Aeropyrum pernix K1 by acetone treatment.	Cong F, Xing K, Gao R, Cao S, Zhang G.	Appl Biochem Biotechnol	10.1007/s12010-011-9297-9	2011
	Characterization of 2-phenanthroate:CoA ligase from the sulfate-reducing, phenanthrene-degrading enrichment culture TRIP.	Kaplieva-Dudek I, Samak NA, Bormann J, Kaschani F, Kaiser M, Meckenstock RU.	Appl Environ Microbiol	10.1128/aem.01296-24	2024
Enzymology	Extracellular production of the engineered thermostable protease pernisine from Aeropyrum pernix K1 in Streptomyces rimosus.	Snajder M, Carrillo Rincon AF, Magdevska V, Bahun M, Kranjc L, Pas M, Juntes P, Petkovic H, Poklar Ulrih N.	Microb Cell Fact	10.1186/s12934-019-1245-3	2019
	Structural properties of archaeal lipid bilayers: small-angle X-ray scattering and molecular dynamics simulation study.	Polak A, Tarek M, Tomsic M, Valant J, Ulrih NP, Jamnik A, Kramar P, Miklavcic D.	Langmuir	10.1021/la5014208	2014
	Bending elasticity modulus of giant vesicles composed of aeropyrum pernix k1 archaeal lipid.	Genova J, Ulrih NP, Kralj-Iglic V, Iglic A, Bivas I.	Life (Basel)	10.3390/life5021101	2015
	Functional characterization of a manganese superoxide dismutase from Avicennia marina: insights into its role in salt, hydrogen peroxide, and heavy metal tolerance.	Abedi H, Shahpiri A.	Sci Rep	10.1038/s41598-023-50851-5	2024
Genetics	Unique architecture of thermophilic archaeal virus APBV1 and its genome packaging.	Ptchelkine D, Gillum A, Mochizuki T, Lucas-Staat S, Liu Y, Krupovic M, Phillips SEV, Prangishvili D, Huiskonen JT.	Nat Commun	10.1038/s41467-017-01668-0	2017
	Construction of an artificial biosynthetic pathway for hyperextended archaeal membrane lipids in the bacterium Escherichia coli.	Yoshida R, Hemmi H.	Synth Biol (Oxf)	10.1093/synbio/ysaa018	2020
Genetics	Genome variation in the hyperthermophilic archaeon Aeropyrum.	Daifuku T, Yoshida T, Sako Y.	Mob Genet Elements	10.4161/mge.26833	2013
	Stability of diether C(25,25) liposomes from the hyperthermophilic archaeon Aeropyrum pernix K1.	Gmajner D, Ota A, Sentjurc M, Ulrih NP.	Chem Phys Lipids	10.1016/j.chemphyslip.2011.01.005	2011
	Structural basis of tRNA recognition by the widespread OB fold.	Umuhire Juru A, Ghirlando R, Zhang J.	Nat Commun	10.1038/s41467-024-50730-1	2024
	NAD+-dependent synthesis of a 5'-phospho-ADP-ribosylated RNA/DNA cap by RNA 2'-phosphotransferase Tpt1.	Munir A, Banerjee A, Shuman S.	Nucleic Acids Res	10.1093/nar/gky792	2018
Metabolism	Topological plasticity of enzymes involved in disulfide bond formation allows catalysis in either the periplasm or the cytoplasm.	Hatahet F, Ruddock LW.	J Mol Biol	10.1016/j.jmb.2013.04.034	2013
Phylogeny	Ubiquitous distribution of phosphatidylinositol phosphate synthase and archaetidylinositol phosphate synthase in Bacteria and Archaea, which contain inositol phospholipid.	Morii H, Ogawa M, Fukuda K, Taniguchi H.	Biochem Biophys Res Commun	10.1016/j.bbrc.2013.11.054	2014
	Light-triggered biocatalysis using thermophilic enzyme-gold nanoparticle complexes.	Blankschien MD, Pretzer LA, Huschka R, Halas NJ, Gonzalez R, Wong MS.	ACS Nano	10.1021/nn3048445	2013
Phylogeny	Diversity of viruses of the hyperthermophilic archaeal genus Aeropyrum, and isolation of the Aeropyrum pernix bacilliform virus 1, APBV1, the first representative of the family Clavaviridae.	Mochizuki T, Yoshida T, Tanaka R, Forterre P, Sako Y, Prangishvili D.	Virology	10.1016/j.virol.2010.03.046	2010
	Involvement of ArlI, ArlJ, and CirA in archaeal type IV pilin-mediated motility regulation.	Chatterjee P, Garcia MA, Cote JA, Yun K, Legerme GP, Habib R, Tripepi M, Young C, Kulp D, Dyall-Smith M, Pohlschroder M.	J Bacteriol	10.1128/jb.00089-24	2024
	Rooted tRNAomes and evolution of the genetic code.	Pak D, Du N, Kim Y, Sun Y, Burton ZF.	Transcription	10.1080/21541264.2018.1429837	2018
Metabolism	Overexpression, purification, and characterization of beta-subunit group II chaperonin from hyperthermophilic Aeropyrum pernix K1.	Shin EJ, Lee JW, Kim JH, Jeon SJ, Kim YH, Nam SW.	J Microbiol Biotechnol	10.4014/jmb.0909.09025	2010
	In silico insights into the dimer structure and deiodinase activity of type III iodothyronine deiodinase from bioinformatics, molecular dynamics simulations, and QM/MM calculations.	Marsan ES, Dreab A, Bayse CA.	J Biomol Struct Dyn	10.1080/07391102.2022.2073271	2023
	Landscape of RNA pseudouridylation in archaeon Sulfolobus islandicus.	Li Y, Wu S, Ye K.	Nucleic Acids Res	10.1093/nar/gkae096	2024
Metabolism	NAD⁺-dependent RNA terminal 2' and 3' phosphomonoesterase activity of a subset of Tpt1 enzymes.	Munir A, Abdullahu L, Banerjee A, Damha MJ, Shuman S.	RNA	10.1261/rna.071142.119	2019
Enzymology	Recombinant purine nucleoside phosphorylases from thermophiles: preparation, properties and activity towards purine and pyrimidine nucleosides.	Zhou X, Szeker K, Janocha B, Bohme T, Albrecht D, Mikhailopulo IA, Neubauer P.	FEBS J	10.1111/febs.12143	2013
Enzymology	Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analyses of threonyl-tRNA synthetase editing domain from Aeropyrum pernix.	Ahmad S, Sravankumar AS, Kruparani SP, Sankaranarayanan R.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309112042066	2012
Metabolism	Thermodynamic and kinetic stability of a large multi-domain enzyme from the hyperthermophile Aeropyrum pernix.	Karlstrom M, Chiaraluce R, Giangiacomo L, Steen IH, Birkeland NK, Ladenstein R, Consalvi V.	Extremophiles	10.1007/s00792-009-0300-0	2010
	Effect of different fluorescent dyes on thermal stability of DNA and cell viability of the hyperthermophilic archaeon Aeropyrum pernix	Crnigoj M, Kostanjsek R, Kaletunc G, Poklar Ulrih N.	World J Microbiol Biotechnol	10.1007/s11274-008-9717-3	2008
	Comparative computational study to augment UbiA prenyltransferases inherent in purple photosynthetic bacteria cultured from mangrove microbial mats in Qatar for coenzyme Q₁₀ biosynthesis.	George DM, Ramadoss R, Mackey HR, Vincent AS.	Biotechnol Rep (Amst)	10.1016/j.btre.2022.e00775	2022
	DeepTracer-ID: De novo protein identification from cryo-EM maps.	Chang L, Wang F, Connolly K, Meng H, Su Z, Cvirkaite-Krupovic V, Krupovic M, Egelman EH, Si D.	Biophys J	10.1016/j.bpj.2022.06.025	2022
	Diverse Engineered Heme Proteins Enable Stereodivergent Cyclopropanation of Unactivated Alkenes.	Knight AM, Kan SBJ, Lewis RD, Brandenberg OF, Chen K, Arnold FH.	ACS Cent Sci	10.1021/acscentsci.7b00548	2018
Metabolism	A Novel Cold-Adapted and Salt-Tolerant RNase R from Antarctic Sea-Ice Bacterium Psychrobacter sp. ANT206.	Wang Y, Hou Y, Nie P, Wang Y, Ren X, Wei Q, Wang Q.	Molecules	10.3390/molecules24122229	2019
Metabolism	Expression and characterization of thymine-DNA glycosylase from Aeropyrum pernix.	Liu XP, Li CP, Hou JL, Liu YF, Liang RB, Liu JH.	Protein Expr Purif	10.1016/j.pep.2009.10.006	2010
	tRNA Misacylation with Methionine in the Mouse Gut Microbiome in Situ.	Schwartz MH, Pan T.	Microb Ecol	10.1007/s00248-016-0928-0	2017
	Cholesterol modulates the structural dynamics of the paddle motif loop of KvAP voltage sensor.	Das A, Bysack A, Raghuraman H.	Curr Res Struct Biol	10.1016/j.crstbi.2024.100137	2024
Metabolism	Membrane-perturbing properties of two Arg-rich paddle domains from voltage-gated sensors in the KvAP and HsapBK K(+) channels.	Unnerstale S, Madani F, Graslund A, Maler L.	Biochemistry	10.1021/bi300188t	2012
	In Silico Structural Modeling and Analysis of Elongation Factor-1 Alpha and Elongation Factor-like Protein.	Sakamoto K, Kayanuma M, Inagaki Y, Hashimoto T, Shigeta Y.	ACS Omega	10.1021/acsomega.8b03547	2019
Metabolism	Two complementary enzymes for threonylation of tRNA in crenarchaeota: crystal structure of Aeropyrum pernix threonyl-tRNA synthetase lacking a cis-editing domain.	Shimizu S, Juan EC, Sato Y, Miyashita Y, Hoque MM, Suzuki K, Sagara T, Tsunoda M, Sekiguchi T, Dock-Bregeon AC, Moras D, Takenaka A.	J Mol Biol	10.1016/j.jmb.2009.09.018	2009
	Structure of a filamentous virus uncovers familial ties within the archaeal virosphere.	Wang F, Baquero DP, Su Z, Osinski T, Prangishvili D, Egelman EH, Krupovic M.	Virus Evol	10.1093/ve/veaa023	2020
Genetics	A Well-Conserved Archaeal B-Family Polymerase Functions as an Extender in Translesion Synthesis.	Feng X, Zhang B, Gao Z, Xu R, Liu X, Ishino S, Feng M, Shen Y, Ishino Y, She Q.	mBio	10.1128/mbio.02659-21	2022
	Recognition and cleavage mechanism of intron-containing pre-tRNA by human TSEN endonuclease complex.	Yuan L, Han Y, Zhao J, Zhang Y, Sun Y.	Nat Commun	10.1038/s41467-023-41845-y	2023
Metabolism	Genome-wide identification and expression profiling of Alba gene family members in response to abiotic stress in tomato (Solanum lycopersicum L.).	Wai AH, Cho LH, Peng X, Waseem M, Lee DJ, Lee JM, Kim CK, Chung MY.	BMC Plant Biol	10.1186/s12870-021-03310-0	2021
Enzymology	Refolding, characterization and crystal structure of (S)-malate dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix.	Kawakami R, Sakuraba H, Goda S, Tsuge H, Ohshima T.	Biochim Biophys Acta	10.1016/j.bbapap.2009.06.014	2009
Metabolism	Biochemical characterization of the minichromosome maintenance (MCM) protein of the crenarchaeote Aeropyrum pernix and its interactions with the origin recognition complex (ORC) proteins.	Atanassova N, Grainge I.	Biochemistry	10.1021/bi801479s	2008
	Interplay between Alba and Cren7 Regulates Chromatin Compaction in Sulfolobus solfataricus.	Cajili MKM, Prieto EI.	Biomolecules	10.3390/biom12040481	2022
Biotechnology	Biochemical and Structural Characterisation of a Novel D-Lyxose Isomerase From the Hyperthermophilic Archaeon Thermofilum sp.	De Rose SA, Kuprat T, Isupov MN, Reinhardt A, Schonheit P, Littlechild JA.	Front Bioeng Biotechnol	10.3389/fbioe.2021.711487	2021
Genetics	Coevolutionary and Phylogenetic Analysis of Mimiviral Replication Machinery Suggest the Cellular Origin of Mimiviruses.	Patil S, Kondabagil K.	Mol Biol Evol	10.1093/molbev/msab003	2021
	Molecular architecture and functional dynamics of the pre-incision complex in nucleotide excision repair.	Yu J, Yan C, Paul T, Brewer L, Tsutakawa SE, Tsai CL, Hamdan SM, Tainer JA, Ivanov I.	Nat Commun	10.1038/s41467-024-52860-y	2024
	Exploring the enzyme-catalyzed synthesis of isotope labeled cyclopropanes.	Sardana M, Muhlfenzl KS, Wenker STM, Akesson C, Hayes MA, Elmore CS, Pithani S.	J Labelled Comp Radiopharm	10.1002/jlcr.3962	2022
Metabolism	Protease cleavage site fingerprinting by label-free in-gel degradomics reveals pH-dependent specificity switch of legumain.	Vidmar R, Vizovisek M, Turk D, Turk B, Fonovic M.	EMBO J	10.15252/embj.201796750	2017
	A pipeline for identification of causal mutations in barley identifies Xantha-j as the chlorophyll synthase gene.	Stuart D, Zakhrabekova S, Jorgensen ME, Dockter C, Hansson M.	Plant Physiol	10.1093/plphys/kiae218	2024
	Biochemical characterization of DNA-binding proteins from Pyrobaculum aerophilum and Aeropyrum pernix.	Hardy CD, Martin PK.	Extremophiles	10.1007/s00792-007-0120-z	2008
Enzymology	Thermophilic archaeal enzymes and applications in biocatalysis.	Littlechild JA.	Biochem Soc Trans	10.1042/bst0390155	2011
	Computational Characterization of Small Molecules Binding to the Human XPF Active Site and Virtual Screening to Identify Potential New DNA Repair Inhibitors Targeting the ERCC1-XPF Endonuclease.	Gentile F, Barakat KH, Tuszynski JA.	Int J Mol Sci	10.3390/ijms19051328	2018
Metabolism	Aeropyrum pernix membrane topology of protein VKOR promotes protein disulfide bond formation in two subcellular compartments.	Hibender S, Landeta C, Berkmen M, Beckwith J, Boyd D.	Microbiology (Reading)	10.1099/mic.0.000569	2017
Metabolism	Reconstruction of the "Archaeal" Mevalonate Pathway from the Methanogenic Archaeon Methanosarcina mazei in Escherichia coli Cells.	Yoshida R, Yoshimura T, Hemmi H.	Appl Environ Microbiol	10.1128/aem.02889-19	2020
Metabolism	A novel class of protease targets of phosphatidylethanolamine-binding proteins (PEBP): a study of the acylpeptide hydrolase and the PEBP inhibitor from the archaeon Sulfolobus solfataricus.	Palmieri G, Langella E, Gogliettino M, Saviano M, Pocsfalvi G, Rossi M.	Mol Biosyst	10.1039/c005293k	2010
Metabolism	Structure of peroxiredoxin from the anaerobic hyperthermophilic archaeon Pyrococcus horikoshii.	Nakamura T, Mori A, Niiyama M, Matsumura H, Tokuyama C, Morita J, Uegaki K, Inoue T.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309113014036	2013
Enzymology	Cryo-EM structure of the KvAP channel reveals a non-domain-swapped voltage sensor topology.	Tao X, MacKinnon R.	Elife	10.7554/elife.52164	2019
Stress	In vivo characterization of thermal stabilities of Aeropyrum pernix cellular components by differential scanning calorimetry.	Milek I, Crnigoj M, Ulrih NP, Kaletunc G.	Can J Microbiol	10.1139/w07-069	2007
	Temperature- and pH-induced structural changes in the membrane of the hyperthermophilic archaeon Aeropyrum pernix K1.	Ulrih NP, Adamlje U, Nemec M, Sentjurc M.	J Membr Biol	10.1007/s00232-007-9061-9	2007
Metabolism	A single amino acid substitution in the DNA-binding domain of Aeropyrum pernix DNA ligase impairs its interaction with proliferating cell nuclear antigen.	Kiyonari S, Kamigochi T, Ishino Y.	Extremophiles	10.1007/s00792-007-0083-0	2007
Enzymology	Crystallization and preliminary X-ray analysis of a dye-linked D-lactate dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix.	Shibahara T, Satomura T, Kawakami R, Ohshima T, Sakuraba H.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309111036098	2011
Enzymology	Glyceraldehyde-3-phosphate ferredoxin oxidoreductase (GAPOR) and nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN), key enzymes of the respective modified Embden-Meyerhof pathways in the hyperthermophilic crenarchaeota Pyrobaculum aerophilum and Aeropyrum pernix.	Reher M, Gebhard S, Schonheit P.	FEMS Microbiol Lett	10.1111/j.1574-6968.2007.00787.x	2007
Metabolism	Specific interactions of three proliferating cell nuclear antigens with replication-related proteins in Aeropyrum pernix.	Imamura K, Fukunaga K, Kawarabayasi Y, Ishino Y.	Mol Microbiol	10.1111/j.1365-2958.2007.05645.x	2007
Metabolism	A conserved lysine residue in the crenarchaea-specific loop is important for the crenarchaeal splicing endonuclease activity.	Okuda M, Shiba T, Inaoka DK, Kita K, Kurisu G, Mineki S, Harada S, Watanabe Y, Yoshinari S.	J Mol Biol	10.1016/j.jmb.2010.10.050	2011
Enzymology	Cysteine synthase: multiple structures of a key enzyme in cysteine synthesis and a potential drug target for Chagas disease and leishmaniasis.	Sowerby K, Freitag-Pohl S, Murillo AM, Silber AM, Pohl E.	Acta Crystallogr D Struct Biol	10.1107/s2059798323003613	2023
	Dissection of Functional Domains of Orc1-2, the Archaeal Global DNA Damage-Responsive Regulator.	Liu X, Sun M, Xu R, Shen Y, Huang Q, Feng X, She Q.	Int J Mol Sci	10.3390/ijms232314609	2022
Metabolism	Reciprocal allostery arising from a bienzyme assembly controls aromatic amino acid biosynthesis in Prevotella nigrescens.	Bai Y, Parker EJ.	J Biol Chem	10.1016/j.jbc.2021.101038	2021
Enzymology	Crystallization and preliminary X-ray analysis of a novel dye-linked L-proline dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix.	Satomura T, Sakuraba H, Hara Y, Ohshima T.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309110036808	2010
	The conserved XPF:ERCC1-like Zip2:Spo16 complex controls meiotic crossover formation through structure-specific DNA binding.	Arora K, Corbett KD.	Nucleic Acids Res	10.1093/nar/gky1273	2019
	Characterization of tRNA splicing enzymes RNA ligase and tRNA 2'-phosphotransferase from the pathogenic fungi Mucorales.	Ghosh S, Dantuluri S, Jacewicz A, Sanchez AM, Abdullahu L, Damha MJ, Schwer B, Shuman S.	RNA	10.1261/rna.079911.123	2024
Enzymology	A novel member of the protein disulfide oxidoreductase family from Aeropyrum pernix K1: structure, function and electrostatics.	D'Ambrosio K, Pedone E, Langella E, De Simone G, Rossi M, Pedone C, Bartolucci S.	J Mol Biol	10.1016/j.jmb.2006.07.038	2006
	A role for [Fe4S4] clusters in tRNA recognition--a theoretical study.	Stiebritz MT.	Nucleic Acids Res	10.1093/nar/gku227	2014
Enzymology	Structural and mechanistic insights into the biosynthesis of CDP-archaeol in membranes.	Ren S, Caforio A, Yang Q, Sun B, Yu F, Zhu X, Wang J, Dou C, Fu Q, Huang N, Sun Q, Nie C, Qi S, Gong X, He J, Wei Y, Driessen AJ, Cheng W.	Cell Res	10.1038/cr.2017.122	2017
Metabolism	Structural Flexibility of Peripheral Loops and Extended C-terminal Domain of Short Length Substrate Binding Protein from Rhodothermus marinus.	Bae JE, Kim IJ, Xu Y, Nam KH.	Protein J	10.1007/s10930-021-09970-z	2021
Metabolism	Biochemical analysis of a DNA replication origin in the archaeon Aeropyrum pernix.	Grainge I, Gaudier M, Schuwirth BS, Westcott SL, Sandall J, Atanassova N, Wigley DB.	J Mol Biol	10.1016/j.jmb.2006.07.076	2006
	Biophysical studies of the membrane location of the voltage-gated sensors in the HsapBK and KvAP K(+) channels.	Biverstahl H, Lind J, Bodor A, Maler L.	Biochim Biophys Acta	10.1016/j.bbamem.2009.07.001	2009
Metabolism	Switch of the interactions between the ribosomal stalk and EF1A in the GTP- and GDP-bound conformations.	Maruyama K, Imai H, Kawamura M, Ishino S, Ishino Y, Ito K, Uchiumi T.	Sci Rep	10.1038/s41598-019-51266-x	2019
	Optimization of growth for the hyperthermophilic archaeon Aeropyrum pernix on a small-batch scale.	Milek I, Cigic B, Skrt M, Kaletunc G, Ulrih NP.	Can J Microbiol	10.1139/w05-060	2005
Metabolism	Identification of the first archaeal oligopeptide-binding protein from the hyperthermophile Aeropyrum pernix.	Palmieri G, Casbarra A, Fiume I, Catara G, Capasso A, Marino G, Onesti S, Rossi M.	Extremophiles	10.1007/s00792-006-0508-1	2006
	Cryo-EM structure of acylpeptide hydrolase reveals substrate selection by multimerization and a multi-state serine-protease triad.	Kiss-Szeman AJ, Straner P, Jakli I, Hosogi N, Harmat V, Menyhard DK, Perczel A.	Chem Sci	10.1039/d2sc02276a	2022
Genetics	The genomics of LUCA.	Mat WK, Xue H, Wong JT.	Front Biosci	10.2741/3103	2008
Metabolism	Directed evolution of prenylated FMN-dependent Fdc supports efficient in vivo isobutene production.	Saaret A, Villiers B, Stricher F, Anissimova M, Cadillon M, Spiess R, Hay S, Leys D.	Nat Commun	10.1038/s41467-021-25598-0	2021
	Revisiting sulfur H-bonds in proteins: The example of peroxiredoxin AhpE.	van Bergen LA, Alonso M, Pallo A, Nilsson L, De Proft F, Messens J.	Sci Rep	10.1038/srep30369	2016
	Temperature dependent mistranslation in a hyperthermophile adapts proteins to lower temperatures.	Schwartz MH, Pan T.	Nucleic Acids Res	10.1093/nar/gkv1379	2016
	Strained Conformations of Nucleosides in Active Sites of Nucleoside Phosphorylases.	Il'icheva IA, Polyakov KM, Mikhailov SN.	Biomolecules	10.3390/biom10040552	2020
	Construction of a novel MK-4 biosynthetic pathway in Pichia pastoris through heterologous expression of HsUBIAD1.	Sun X, Liu H, Wang P, Wang L, Ni W, Yang Q, Wang H, Tang H, Zhao G, Zheng Z.	Microb Cell Fact	10.1186/s12934-019-1215-9	2019
Genetics	Variation of the virus-related elements within syntenic genomes of the hyperthermophilic Archaeon Aeropyrum.	Daifuku T, Yoshida T, Kitamura T, Kawaichi S, Inoue T, Nomura K, Yoshida Y, Kuno S, Sako Y.	Appl Environ Microbiol	10.1128/aem.01089-13	2013
Metabolism	Gene recognition based on nucleotide distribution of ORFs in a hyper-thermophilic crenarchaeon, Aeropyrum pernix K1.	Guo FB, Wang J, Zhang CT.	DNA Res	10.1093/dnares/11.6.361	2004
Metabolism	Structure of tRNA splicing enzyme Tpt1 illuminates the mechanism of RNA 2'-PO₄ recognition and ADP-ribosylation.	Banerjee A, Munir A, Abdullahu L, Damha MJ, Goldgur Y, Shuman S.	Nat Commun	10.1038/s41467-018-08211-9	2019
	Provirus induction in hyperthermophilic archaea: characterization of Aeropyrum pernix spindle-shaped virus 1 and Aeropyrum pernix ovoid virus 1.	Mochizuki T, Sako Y, Prangishvili D.	J Bacteriol	10.1128/jb.05101-11	2011
Enzymology	Crystallization of the xeroderma pigmentosum group F endonuclease from Aeropyrum pernix.	Lally J, Newman M, Murray-Rust J, Fadden A, Kawarabayasi Y, McDonald N.	Acta Crystallogr D Biol Crystallogr	10.1107/s0907444904016968	2004
	Structural and kinetic contributions of the oxyanion binding site to the catalytic activity of acylaminoacyl peptidase.	Kiss AL, Pallo A, Naray-Szabo G, Harmat V, Polgar L.	J Struct Biol	10.1016/j.jsb.2008.01.012	2008
Genetics	Determination of the Amino Acid Recruitment Order in Early Life by Genome-Wide Analysis of Amino Acid Usage Bias.	Zhao M, Ding R, Liu Y, Ji Z, Zhao Y.	Biomolecules	10.3390/biom12020171	2022
Enzymology	Peroxiredoxins as cellular guardians in Sulfolobus solfataricus: characterization of Bcp1, Bcp3 and Bcp4.	Limauro D, Pedone E, Galdi I, Bartolucci S.	FEBS J	10.1111/j.1742-4658.2008.06361.x	2008
Metabolism	Conformational changes induced by nucleotide binding in Cdc6/ORC from Aeropyrum pernix.	Singleton MR, Morales R, Grainge I, Cook N, Isupov MN, Wigley DB.	J Mol Biol	10.1016/j.jmb.2004.08.044	2004
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Enzymology	The microbial ecology of a high-temperature near-neutral spring situated in Rotorua, New Zealand.	Niederberger TD, Ronimus RS, Morgan HW.	Microbiol Res	10.1016/j.micres.2006.09.001	2008
Metabolism	Oxidized Substrates of APEH as a Tool to Study the Endoprotease Activity of the Enzyme.	Sandomenico A, Gogliettino M, Iaccarino E, Fusco C, Caporale A, Ruvo M, Palmieri G, Cocca E.	Int J Mol Sci	10.3390/ijms23010443	2021
Enzymology	A preliminary solubility screen used to improve crystallization trials: crystallization and preliminary X-ray structure determination of Aeropyrum pernix flap endonuclease-1.	Collins BK, Tomanicek SJ, Lyamicheva N, Kaiser MW, Mueser TC.	Acta Crystallogr D Biol Crystallogr	10.1107/s090744490401844x	2004
Genetics	Plasmid Library Construction From Genomic DNA.	Florez-Cardona V, Khani J, McNutt E, Manta B, Berkmen M.	Curr Protoc	10.1002/cpz1.70088	2025
Enzymology	Alteration of product specificity of Aeropyrum pernix farnesylgeranyl diphosphate synthase (Fgs) by directed evolution.	Lee PC, Mijts BN, Petri R, Watts KT, Schmidt-Dannert C.	Protein Eng Des Sel	10.1093/protein/gzh089	2004
	Exploring functional and structural features of chemically related natural prenylated hydroquinone and benzoic acid from Piper crassinervium (Piperaceae) on bacterial peroxiredoxin inhibition.	Montanhero Cabrera VI, do Nascimento Sividanes G, Quintiliano NF, Hikari Toyama M, Ghilardi Lago JH, de Oliveira MA.	PLoS One	10.1371/journal.pone.0281322	2023
	A Novel Family of Winged-Helix Single-Stranded DNA-Binding Proteins from Archaea.	Huang C, Liu X, Chen Y, Zhou J, Li W, Ding N, Huang L, Chen J, Zhang Z.	Int J Mol Sci	10.3390/ijms23073455	2022
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Metabolism	Voltage vs. Ligand II: Structural insights of the intrinsic flexibility in cyclic nucleotide-gated channels.	Romero-Romero S, Martinez-Delgado G, Balleza D.	Channels (Austin)	10.1080/19336950.2019.1666456	2019
Enzymology	A Hitchhiker's Guide to Supplying Enzymatic Reducing Power into Synthetic Cells.	Partipilo M, Claassens NJ, Slotboom DJ.	ACS Synth Biol	10.1021/acssynbio.3c00070	2023
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Metabolism	Crystal structure and RNA-binding analysis of the archaeal transcription factor NusA.	Shibata R, Bessho Y, Shinkai A, Nishimoto M, Fusatomi E, Terada T, Shirouzu M, Yokoyama S.	Biochem Biophys Res Commun	10.1016/j.bbrc.2007.01.119	2007
Enzymology	Isocitrate dehydrogenase from the hyperthermophile Aeropyrum pernix: X-ray structure analysis of a ternary enzyme-substrate complex and thermal stability.	Karlstrom M, Stokke R, Steen IH, Birkeland NK, Ladenstein R.	J Mol Biol	10.1016/j.jmb.2004.10.025	2005
Enzymology	Overexpression of the genes from thermophiles in Escherichia coli by high-temperature cultivation.	Koma D, Sawai T, Harayama S, Kino K.	Appl Microbiol Biotechnol	10.1007/s00253-006-0448-9	2006
Enzymology	Crystallization and preliminary crystallographic analysis of a putative glucokinase/hexokinase from Thermus thermophilus.	Nakamura T, Kashima Y, Mine S, Oku T, Uegaki K.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309111041145	2011
Metabolism	A Phosphofructokinase Homolog from Pyrobaculum calidifontis Displays Kinase Activity towards Pyrimidine Nucleosides and Ribose 1-Phosphate.	Aziz I, Bibi T, Rashid N, Aono R, Atomi H, Akhtar M.	J Bacteriol	10.1128/jb.00284-18	2018
Transcriptome	On the existence of wavelet symmetries in archaea DNA.	Cattani C.	Comput Math Methods Med	10.1155/2012/673934	2012
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Enzymology	Thermal stability of isocitrate dehydrogenase from Archaeoglobus fulgidus studied by crystal structure analysis and engineering of chimers.	Stokke R, Karlstrom M, Yang N, Leiros I, Ladenstein R, Birkeland NK, Steen IH.	Extremophiles	10.1007/s00792-006-0060-z	2007
Pathogenicity	In Silico analysis of voltage-gated sodium channel in relation to DDT resistance in vector mosquitoes.	Rajesh R, Gunasekaran K, Muthukumaravel S, Balaraman K, Jambulingam P.	In Silico Biol	10.3233/isi-2007-00299	2007
Enzymology	Streptomycetes: Attractive Hosts for Recombinant Protein Production.	Berini F, Marinelli F, Binda E.	Front Microbiol	10.3389/fmicb.2020.01958	2020
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Enzymology	Bifunctional phosphoglucose/phosphomannose isomerases from the Archaea Aeropyrum pernix and Thermoplasma acidophilum constitute a novel enzyme family within the phosphoglucose isomerase superfamily.	Hansen T, Wendorff D, Schonheit P.	J Biol Chem	10.1074/jbc.m309849200	2004
Enzymology	Thermal stability and biochemical properties of isocitrate dehydrogenase from the thermoacidophilic archaeon Thermoplasma acidophilum.	Stokke R, Birkeland NK, Steen IH.	Extremophiles	10.1007/s00792-006-0045-y	2007
Enzymology	The structure of an alcohol dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix.	Guy JE, Isupov MN, Littlechild JA.	J Mol Biol	10.1016/s0022-2836(03)00857-x	2003
Enzymology	Crystallization and preliminary crystallographic analysis of acylamino-acid releasing enzyme from the hyperthermophilic archaeon Aeropyrum pernix.	Wang G, Gao R, Ding Y, Yang H, Cao S, Feng Y, Rao Z.	Acta Crystallogr D Biol Crystallogr	10.1107/s0907444902005875	2002
Metabolism	The phosphofructokinase-B (MJ0406) from Methanocaldococcus jannaschii represents a nucleoside kinase with a broad substrate specificity.	Hansen T, Arnfors L, Ladenstein R, Schonheit P.	Extremophiles	10.1007/s00792-006-0018-1	2007
Enzymology	Crystal structure of glutamate-1-semialdehyde-2,1-aminomutase from Arabidopsis thaliana.	Song Y, Pu H, Jiang T, Zhang L, Ouyang M.	Acta Crystallogr F Struct Biol Commun	10.1107/s2053230x16007263	2016
	Lack of Periplasmic Non-heme Protein SorA Increases Shewanella decolorationis Current Generation.	Kong G, Song D, Guo J, Sun G, Zhu C, Chen F, Yang Y, Xu M.	Front Microbiol	10.3389/fmicb.2020.00262	2020
Enzymology	Crystallization and preliminary X-ray structure analysis of isocitrate dehydrogenase from two hyperthermophiles, Aeropyrum pernix and Thermotoga maritima.	Karlstrom M, Steen IH, Tibbelin G, Lien T, Birkeland NK, Ladenstein R.	Acta Crystallogr D Biol Crystallogr	10.1107/s0907444902016050	2002
Enzymology	Characterization of novel hexadecameric thioredoxin peroxidase from Aeropyrum pernix K1.	Jeon SJ, Ishikawa K.	J Biol Chem	10.1074/jbc.m300618200	2003
Metabolism	Purification and biochemical properties of a cytochrome bc complex from the aerobic hyperthermophilic archaeon Aeropyrum pernix.	Kabashima Y, Sakamoto J.	BMC Microbiol	10.1186/1471-2180-11-52	2011
Metabolism	Archaeal pre-mRNA splicing: a connection to hetero-oligomeric splicing endonuclease.	Yoshinari S, Itoh T, Hallam SJ, DeLong EF, Yokobori S, Yamagishi A, Oshima T, Kita K, Watanabe Y.	Biochem Biophys Res Commun	10.1016/j.bbrc.2006.06.011	2006
Enzymology	Crystallization and preliminary X-ray diffraction studies of a novel alcohol dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix.	Guy JE, Isupov MN, Littlechild JA.	Acta Crystallogr D Biol Crystallogr	10.1107/s0907444902019649	2003
Enzymology	Cloning, expression, and characterization of the first archaeal ATP-dependent glucokinase from aerobic hyperthermophilic archaeon Aeropyrum pernix.	Sakuraba H, Mitani Y, Goda S, Kawarabayasi Y, Ohshima T.	J Biochem	10.1093/jb/mvg027	2003
Enzymology	Expression of two kinds of recombinant glutamate dehydrogenase from Aeropyrum pernix with different N-terminal sequence length in Escherichia coli.	Helianti I, Morita Y, Murakami Y, Yokoyama K, Tamiya E.	Appl Microbiol Biotechnol	10.1007/s00253-002-1051-3	2002
	Heterogeneous yet similar introns reside in identical positions of the rRNA genes in natural isolates of the archaeon Aeropyrum pernix.	Nomura N, Morinaga Y, Kogishi T, Kim EJ, Sako Y, Uchida A.	Gene	10.1016/s0378-1119(02)00802-8	2002
Enzymology	Crystal Structures of the Putative Isocitrate Dehydrogenase from Sulfolobus tokodaii Strain 7 in the Apo and NADP⁺-Bound Forms.	Kondo H, Murakami M.	Archaea	10.1155/2018/7571984	2018
	Structure of the Aeropyrum pernix L7Ae multifunctional protein and insight into its extreme thermostability.	Bhuiya MW, Suryadi J, Zhou Z, Brown BA.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309113021799	2013
	G:U-Independent RNA Minihelix Aminoacylation by Nanoarchaeum equitans Alanyl-tRNA Synthetase: An Insight into the Evolution of Aminoacyl-tRNA Synthetases.	Arutaki M, Kurihara R, Matsuoka T, Inami A, Tokunaga K, Ohno T, Takahashi H, Takano H, Ando T, Mutsuro-Aoki H, Umehara T, Tamura K.	J Mol Evol	10.1007/s00239-020-09945-1	2020
Enzymology	Log P effect of organic solvents on a thermophilic alcohol dehydrogenase.	Hirakawa H, Kamiya N, Kawarabayashi Y, Nagamune T.	Biochim Biophys Acta	10.1016/j.bbapap.2004.12.007	2005
Enzymology	Cloning, overexpression, and characterization of a thermoactive nitrilase from the hyperthermophilic archaeon Pyrococcus abyssi.	Mueller P, Egorova K, Vorgias CE, Boutou E, Trauthwein H, Verseck S, Antranikian G.	Protein Expr Purif	10.1016/j.pep.2006.01.006	2006
Enzymology	The first crystal structure of archaeal aldolase. Unique tetrameric structure of 2-deoxy-d-ribose-5-phosphate aldolase from the hyperthermophilic archaea Aeropyrum pernix.	Sakuraba H, Tsuge H, Shimoya I, Kawakami R, Goda S, Kawarabayasi Y, Katunuma N, Ago H, Miyano M, Ohshima T.	J Biol Chem	10.1074/jbc.m212449200	2003
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Enzymology	Comparative analysis of pyruvate kinases from the hyperthermophilic archaea Archaeoglobus fulgidus, Aeropyrum pernix, and Pyrobaculum aerophilum and the hyperthermophilic bacterium Thermotoga maritima: unusual regulatory properties in hyperthermophilic archaea.	Johnsen U, Hansen T, Schonheit P.	J Biol Chem	10.1074/jbc.m210288200	2003
Metabolism	Quorum sensing in thermophiles: prevalence of autoinducer-2 system.	Kaur A, Capalash N, Sharma P.	BMC Microbiol	10.1186/s12866-018-1204-x	2018
Metabolism	Cloning, expression and characterisation of a Family B ATP-dependent phosphofructokinase activity from the hyperthermophilic crenarachaeon Aeropyrum pernix.	Ronimus RS, Kawarabayasi Y, Kikuchi H, Morgan HW.	FEMS Microbiol Lett	10.1111/j.1574-6968.2001.tb10784.x	2001
Stress	High selectivity of the hyperthermophilic subtilase propeptide domain toward inhibition of its cognate protease.	Bahun M, Poklar Ulrih N.	Microbiol Spectr	10.1128/spectrum.01487-23	2023
	Deciphering the Substrate Specificity of SbnA, the Enzyme Catalyzing the First Step in Staphyloferrin B Biosynthesis.	Kobylarz MJ, Grigg JC, Liu Y, Lee MS, Heinrichs DE, Murphy ME.	Biochemistry	10.1021/acs.biochem.5b01045	2016
Metabolism	Active-site plasticity revealed in the asymmetric dimer of AnPrx6 the 1-Cys peroxiredoxin and molecular chaperone from Anabaena sp. PCC 7210.	Mishra Y, Hall M, Locmelis R, Nam K, Soderberg CAG, Storm P, Chaurasia N, Rai LC, Jansson S, Schroder WP, Schroder WP, Sauer UH.	Sci Rep	10.1038/s41598-017-17044-3	2017
Metabolism	The archaeal ATPase PINA interacts with the helicase Hjm via its carboxyl terminal KH domain remodeling and processing replication fork and Holliday junction.	Zhai B, DuPrez K, Han X, Yuan Z, Ahmad S, Xu C, Gu L, Ni J, Fan L, Shen Y.	Nucleic Acids Res	10.1093/nar/gky451	2018
Metabolism	Characterization of MenA (isoprenyl diphosphate:1,4-dihydroxy-2-naphthoate isoprenyltransferase) from Mycobacterium tuberculosis.	Dhiman RK, Pujari V, Kincaid JM, Ikeh MA, Parish T, Crick DC.	PLoS One	10.1371/journal.pone.0214958	2019
	External K+ modulates the activity of the Arabidopsis potassium channel SKOR via an unusual mechanism.	Johansson I, Wulfetange K, Poree F, Michard E, Gajdanowicz P, Lacombe B, Sentenac H, Thibaud JB, Mueller-Roeber B, Blatt MR, Dreyer I.	Plant J	10.1111/j.1365-313x.2006.02690.x	2006
	4-Hydroxybenzoic acid restores CoQ₁₀ biosynthesis in human COQ2 deficiency.	Herebian D, Seibt A, Smits SHJ, Rodenburg RJ, Mayatepek E, Distelmaier F.	Ann Clin Transl Neurol	10.1002/acn3.486	2017
Metabolism	Reversal of Regioselectivity in Zinc-Dependent Medium-Chain Alcohol Dehydrogenase from Rhodococcus erythropolis toward Octanone Derivatives.	Dhoke GV, Ensari Y, Hacibaloglu DY, Gartner A, Ruff AJ, Bocola M, Davari MD.	Chembiochem	10.1002/cbic.202000247	2020
Genetics	Quantifying intrachromosomal GC heterogeneity in prokaryotic genomes.	Bernaola-Galvan P, Oliver JL, Carpena P, Clay O, Bernardi G.	Gene	10.1016/j.gene.2004.02.042	2004
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Metabolism	Sequence, expression, and characterization of the first archaeal ATP-dependent 6-phosphofructokinase, a non-allosteric enzyme related to the phosphofructokinase-B sugar kinase family, from the hyperthermophilic crenarchaeote Aeropyrum pernix.	Hansen T, Schonheit P.	Arch Microbiol	10.1007/s00203-001-0359-1	2001
Metabolism	Diversity of voltage-gated potassium channels and cyclic nucleotide-binding domain-containing channels in eukaryotes.	Pozdnyakov I, Safonov P, Skarlato S.	Sci Rep	10.1038/s41598-020-74971-4	2020
Enzymology	Hyperthermophilic dehydrogenase enzymes.	Littlechild JA, Guy JE, Isupov MN.	Biochem Soc Trans	10.1042/bst0320255	2004
Enzymology	Crystal structures of tyrosyl-tRNA synthetases from Archaea.	Kuratani M, Sakai H, Takahashi M, Yanagisawa T, Kobayashi T, Murayama K, Chen L, Liu ZJ, Wang BC, Kuroishi C, Kuramitsu S, Terada T, Bessho Y, Shirouzu M, Sekine S, Yokoyama S.	J Mol Biol	10.1016/j.jmb.2005.10.073	2006
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Enzymology	Recombinant Enzymatic Redox Systems for Preparation of Aroma Compounds by Biotransformation.	Varga V, Stefuca V, Mihalova L, Levarski Z, Struharnanska E, Blasko J, Kubinec R, Farkas P, Sitkey V, Turna J, Rosenberg M, Stuchlik S.	Front Microbiol	10.3389/fmicb.2021.684640	2021
	Crystal Structure of the Apo-Form of NADPH-Dependent Thioredoxin Reductase from a Methane-Producing Archaeon.	Buey RM, Schmitz RA, Buchanan BB, Balsera M.	Antioxidants (Basel)	10.3390/antiox7110166	2018
Enzymology	Structure and Function of Piezophilic Hyperthermophilic Pyrococcus yayanosii pApase.	Jin Z, Wang W, Li X, Zhou H, Yi G, Wang Q, Yu F, Xiao X, Liu X.	Int J Mol Sci	10.3390/ijms22137159	2021
	Isolation and biochemical characterization of a metagenome-derived 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase gene from subtropical marine mangrove wetland sediments.	Zhao H, Gao H, Ji K, Yan B, Li Q, Mo S, Zheng M, Ou Q, Wu B, Li N, Jiang C.	AMB Express	10.1186/s13568-019-0742-4	2019
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Metabolism	Localization of the voltage-sensor toxin receptor on KvAP.	Ruta V, MacKinnon R.	Biochemistry	10.1021/bi049463y	2004
Enzymology	The RNA-splicing endonuclease from the euryarchaeaon Methanopyrus kandleri is a heterotetramer with constrained substrate specificity.	Kaneta A, Fujishima K, Morikazu W, Hori H, Hirata A.	Nucleic Acids Res	10.1093/nar/gky003	2018
Enzymology	Structure of aldolase from Thermus thermophilus HB8 showing the contribution of oligomeric state to thermostability.	Lokanath NK, Shiromizu I, Ohshima N, Nodake Y, Sugahara M, Yokoyama S, Kuramitsu S, Miyano M, Kunishima N.	Acta Crystallogr D Biol Crystallogr	10.1107/s0907444904020190	2004
Metabolism	A proton pore in a potassium channel voltage sensor reveals a focused electric field.	Starace DM, Bezanilla F.	Nature	10.1038/nature02270	2004
Metabolism	A cell-free translocation system using extracts of cultured insect cells to yield functional membrane proteins.	Ezure T, Nanatani K, Sato Y, Suzuki S, Aizawa K, Souma S, Ito M, Hohsaka T, von Heijine G, Utsumi T, Abe K, Ando E, Uozumi N.	PLoS One	10.1371/journal.pone.0112874	2014
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Enzymology	Structure and characterization of the 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Aeropyrum pernix.	Zhou L, Wu J, Vijayalakshmi J, Shumilin IA, Bauerle R, Kretsinger RH, Woodard RW.	Bioorg Chem	10.1016/j.bioorg.2011.09.002	2012
Phylogeny	Mapping hidden potential identity elements by computing the average discriminating power of individual tRNA positions.	Szenes A, Pal G.	DNA Res	10.1093/dnares/dss008	2012
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Metabolism	De novo transcriptome reveals blood coagulation/antithrombin factors and infection mechanisms in Angiostrongylus cantonensis adult worms.	de Mattos Pereira L, de Jezuz MPG, Rangel AR, Baldasso BD, Zaluski AB, Graeff-Teixeira C, Morassutti AL.	Parasitology	10.1017/s0031182021000469	2021
Enzymology	A cambialistic SOD in a strictly aerobic hyperthermophilic archaeon, Aeropyrum pernix.	Yamano S, Sako Y, Nomura N, Maruyama T.	J Biochem	10.1093/oxfordjournals.jbchem.a022426	1999
Enzymology	Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of AerF from Microcystis aeruginosa, a putative reductase participating in aeruginosin biosynthesis.	Ding R, Xu C, Chen X, Bao M, Qiu X.	Acta Crystallogr F Struct Biol Commun	10.1107/s2053230x15005063	2015
Metabolism	Predominant Acidilobus-like populations from geothermal environments in yellowstone national park exhibit similar metabolic potential in different hypoxic microbial communities.	Jay ZJ, Rusch DB, Tringe SG, Bailey C, Jennings RM, Inskeep WP.	Appl Environ Microbiol	10.1128/aem.02860-13	2014
Enzymology	Engineering a Seven Enzyme Biotransformation using Mathematical Modelling and Characterized Enzyme Parts.	Finnigan W, Cutlan R, Snajdrova R, Adams JP, Littlechild JA, Harmer NJ.	ChemCatChem	10.1002/cctc.201900646	2019
Phylogeny	Transfer RNA paralogs: evidence for genetic code-amino acid biosynthesis coevolution and an archaeal root of life.	Xue H, Tong KL, Marck C, Grosjean H, Wong JT.	Gene	10.1016/s0378-1119(03)00552-3	2003
Metabolism	Novel prenyltransferase gene encoding farnesylgeranyl diphosphate synthase from a hyperthermophilic archaeon, Aeropyrum pernix. Molecularevolution with alteration in product specificity.	Tachibana A, Yano Y, Otani S, Nomura N, Sako Y, Taniguchi M.	Eur J Biochem	10.1046/j.1432-1327.2000.00967.x	2000
	X-ray structure of a voltage-dependent K+ channel.	Jiang Y, Lee A, Chen J, Ruta V, Cadene M, Chait BT, MacKinnon R.	Nature	10.1038/nature01580	2003
	Crystal structure of heme A synthase from Bacillus subtilis.	Niwa S, Takeda K, Kosugi M, Tsutsumi E, Mogi T, Miki K.	Proc Natl Acad Sci U S A	10.1073/pnas.1813346115	2018
Enzymology	A novel phosphoglycolipid archaetidyl(glucosyl)inositol with two sesterterpanyl chains from the aerobic hyperthermophilic archaeon Aeropyrum pernix K1.	Morii H, Yagi H, Akutsu H, Nomura N, Sako Y, Koga Y.	Biochim Biophys Acta	10.1016/s0005-2760(98)00157-x	1999
Enzymology	Propionate CoA-transferase from Clostridium propionicum. Cloning of gene and identification of glutamate 324 at the active site.	Selmer T, Willanzheimer A, Hetzel M.	Eur J Biochem	10.1046/j.0014-2956.2001.02659.x	2002
Enzymology	Crystal structure of novel dye-linked L-proline dehydrogenase from hyperthermophilic archaeon Aeropyrum pernix.	Sakuraba H, Satomura T, Kawakami R, Kim K, Hara Y, Yoneda K, Ohshima T.	J Biol Chem	10.1074/jbc.m111.319038	2012
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Metabolism	Holliday junction-resolving enzymes from eight hyperthermophilic archaea differ in reactions with cruciform DNA.	Neef K, Birkenbihl RP, Kemper B.	Extremophiles	10.1007/s00792-002-0265-8	2002
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Enzymology	Crystallization and preliminary crystallographic studies of putative threonyl-tRNA synthetases from Aeropyrum pernix and Sulfolobus tokodaii.	Shimizu S, Juan EC, Miyashita YI, Sato Y, Hoque MM, Suzuki K, Yogiashi M, Tsunoda M, Dock-Bregeon AC, Moras D, Sekiguchi T, Takenaka A.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309108026924	2008
Metabolism	Characterization of family IV UDG from Aeropyrum pernix and its application in hot-start PCR by family B DNA polymerase.	Liu XP, Liu JH.	PLoS One	10.1371/journal.pone.0027248	2011
Metabolism	The hexokinase of the hyperthermophile Thermoproteus tenax. ATP-dependent hexokinases and ADP-dependent glucokinases, teo alternatives for glucose phosphorylation in Archaea.	Dorr C, Zaparty M, Tjaden B, Brinkmann H, Siebers B.	J Biol Chem	10.1074/jbc.m301914200	2003
Genetics	DNA replication origins in archaea.	Wu Z, Liu J, Yang H, Xiang H.	Front Microbiol	10.3389/fmicb.2014.00179	2014
Metabolism	Global tRNA misacylation induced by anaerobiosis and antibiotic exposure broadly increases stress resistance in Escherichia coli.	Schwartz MH, Waldbauer JR, Zhang L, Pan T.	Nucleic Acids Res	10.1093/nar/gkw856	2016
	Complete atomic structure of a native archaeal cell surface.	von Kugelgen A, Alva V, Bharat TAM.	Cell Rep	10.1016/j.celrep.2021.110052	2021
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Enzymology	The biochemical properties and phylogenies of phosphofructokinases from extremophiles.	Ronimus RS, Morgan HW.	Extremophiles	10.1007/s007920100215	2001
Phylogeny	Updating carbamoylphosphate synthase (CPS) phylogenies: occurrence and phylogenetic identity of archaeal CPS genes.	Cammarano P, Gribaldo S, Johann A.	J Mol Evol	10.1007/s00239-002-2312-6	2002
	Activity and substrate specificity of Candida, Aspergillus, and Coccidioides Tpt1: essential tRNA splicing enzymes and potential antifungal targets.	Dantuluri S, Schwer B, Abdullahu L, Damha MJ, Shuman S.	RNA	10.1261/rna.078660.120	2021
	First Crystal Structure of Bacterial Oligopeptidase B in an Intermediate State: The Roles of the Hinge Region Modification and Spermine.	Petrenko DE, Timofeev VI, Britikov VV, Britikova EV, Kleymenov SY, Vlaskina AV, Kuranova IP, Mikhailova AG, Rakitina TV.	Biology (Basel)	10.3390/biology10101021	2021
Genetics	Using homolog groups to create a whole-genomic tree of free-living organisms: an update.	House CH, Fitz-Gibbon ST.	J Mol Evol	10.1007/s00239-001-0054-5	2002
Genetics	Status of genome projects for nonpathogenic bacteria and archaea.	Nelson KE, Paulsen IT, Heidelberg JF, Fraser CM.	Nat Biotechnol	10.1038/80235	2000
Enzymology	Comparison of isocitrate dehydrogenase from three hyperthermophiles reveals differences in thermostability, cofactor specificity, oligomeric state, and phylogenetic affiliation.	Steen IH, Madern D, Karlstrom M, Lien T, Ladenstein R, Birkeland NK.	J Biol Chem	10.1074/jbc.m105999200	2001
Metabolism	Interactions of archaeal chromatin proteins Alba1 and Alba2 with nucleic acids.	Crnigoj M, Podlesek Z, Zorko M, Jerala R, Anderluh G, Ulrih NP.	PLoS One	10.1371/journal.pone.0058237	2013
	Polerovirus N-terminal readthrough domain structures reveal molecular strategies for mitigating virus transmission by aphids.	Schiltz CJ, Wilson JR, Hosford CJ, Adams MC, Preising SE, DeBlasio SL, MacLeod HJ, Van Eck J, Heck ML, Chappie JS.	Nat Commun	10.1038/s41467-022-33979-2	2022
	Omnipotent role of archaeal elongation factor 1 alpha (EF1alpha in translational elongation and termination, and quality control of protein synthesis.	Saito K, Kobayashi K, Wada M, Kikuno I, Takusagawa A, Mochizuki M, Uchiumi T, Ishitani R, Nureki O, Ito K.	Proc Natl Acad Sci U S A	10.1073/pnas.1009599107	2010
Phylogeny	Phylogenetic analysis of archaeal PCNA homologues.	Iwai T, Kurosawa N, Itoh YH, Horiuchi T.	Extremophiles	10.1007/s007920070005	2000
Pathogenicity	Discovery of ebselen as an inhibitor of Cryptosporidium parvum glucose-6-phosphate isomerase (CpGPI) by high-throughput screening of existing drugs.	Eltahan R, Guo F, Zhang H, Xiang L, Zhu G.	Int J Parasitol Drugs Drug Resist	10.1016/j.ijpddr.2018.01.003	2018
Metabolism	Identification of a Direct Biosynthetic Pathway for UDP-N-Acetylgalactosamine from Glucosamine-6-Phosphate in Thermophilic Crenarchaeon Sulfolobus tokodaii.	Dadashipour M, Iwamoto M, Hossain MM, Akutsu JI, Zhang Z, Kawarabayasi Y.	J Bacteriol	10.1128/jb.00048-18	2018
Metabolism	A Mutant Chaperonin That Is Functional at Lower Temperatures Enables Hyperthermophilic Archaea To Grow under Cold-Stress Conditions.	Gao L, Imanaka T, Fujiwara S.	J Bacteriol	10.1128/jb.00279-15	2015
Enzymology	Crystal structures of aconitase X enzymes from bacteria and archaea provide insights into the molecular evolution of the aconitase superfamily.	Watanabe S, Murase Y, Watanabe Y, Sakurai Y, Tajima K.	Commun Biol	10.1038/s42003-021-02147-5	2021
Metabolism	Active site of Zn(2+)-dependent sn-glycerol-1-phosphate dehydrogenase from Aeropyrum pernix K1.	Han JS, Ishikawa K.	Archaea	10.1155/2005/257264	2005
	ADP-ribosylation of RNA in mammalian cells is mediated by TRPT1 and multiple PARPs.	Weixler L, Feijs KLH, Zaja R.	Nucleic Acids Res	10.1093/nar/gkac711	2022
Enzymology	Characterization of a cold-active, detergent-stable metallopeptidase purified from Bacillus sp. S1DI 10 using Response Surface Methodology.	Singh D, Thakur S, Thayil SM, Kesavan AK.	PLoS One	10.1371/journal.pone.0216990	2019
Enzymology	Recombinant superoxide dismutase from a hyperthermophilic archaeon, Pyrobaculum aerophilium.	Whittaker MM, Whittaker JW.	J Biol Inorg Chem		2000
Enzymology	Purification, crystallization and preliminary crystallographic analysis of a multiple cofactor-dependent DNA ligase from Sulfophobococcus zilligii.	Supangat S, An YJ, Sun Y, Kwon ST, Cha SS.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309110034135	2010
	Discovery of permuted and recently split transfer RNAs in Archaea.	Chan PP, Cozen AE, Lowe TM.	Genome Biol	10.1186/gb-2011-12-4-r38	2011
Enzymology	Tyrosine substitution of a conserved active-site histidine residue activates Plasmodium falciparum peroxiredoxin 6.	Feld K, Geissel F, Liedgens L, Schumann R, Specht S, Deponte M.	Protein Sci	10.1002/pro.3490	2019
Metabolism	Cleavage of intron from the standard or non-standard position of the precursor tRNA by the splicing endonuclease of Aeropyrum pernix, a hyper-thermophilic Crenarchaeon, involves a novel RNA recognition site in the Crenarchaea specific loop.	Hirata A, Kitajima T, Hori H.	Nucleic Acids Res	10.1093/nar/gkr615	2011
Enzymology	Production, crystallization and preliminary X-ray analysis of CTP:inositol-1-phosphate cytidylyltransferase from Archaeoglobus fulgidus.	Brito JA, Borges N, Santos H, Archer M.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309110032677	2010
Metabolism	The terminal 5' phosphate and proximate phosphorothioate promote ligation-independent cloning.	Liu XP, Liu JH.	Protein Sci	10.1002/pro.374	2010
	Genomic Insight of Alicyclobacillus mali FL18 Isolated From an Arsenic-Rich Hot Spring.	Aulitto M, Gallo G, Puopolo R, Mormone A, Limauro D, Contursi P, Piochi M, Bartolucci S, Fiorentino G.	Front Microbiol	10.3389/fmicb.2021.639697	2021
Metabolism	Glucose Metabolism and Acetate Switch in Archaea: the Enzymes in Haloferax volcanii.	Kuprat T, Ortjohann M, Johnsen U, Schonheit P.	J Bacteriol	10.1128/jb.00690-20	2021
	Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome.	Mochizuki T, Krupovic M, Pehau-Arnaudet G, Sako Y, Forterre P, Prangishvili D.	Proc Natl Acad Sci U S A	10.1073/pnas.1203668109	2012
	Extrachromosomal element capture and the evolution of multiple replication origins in archaeal chromosomes.	Robinson NP, Bell SD.	Proc Natl Acad Sci U S A	10.1073/pnas.0700206104	2007
	Identifying the ligated amino acid of archaeal tRNAs based on positions outside the anticodon.	Galili T, Gingold H, Shaul S, Benjamini Y.	RNA	10.1261/rna.053777.115	2016
Enzymology	Two-step mechanism and step-arrest mutants of Runella slithyformis NAD⁺-dependent tRNA 2'-phosphotransferase Tpt1.	Munir A, Abdullahu L, Damha MJ, Shuman S.	RNA	10.1261/rna.067165.118	2018
	A new family of bacterial ribosome hibernation factors.	Helena-Bueno K, Rybak MY, Ekemezie CL, Sullivan R, Brown CR, Dingwall C, Basle A, Schneider C, Connolly JPR, Blaza JN, Csorgo B, Moynihan PJ, Gagnon MG, Hill CH, Melnikov SV.	Nature	10.1038/s41586-024-07041-8	2024
Metabolism	Voltage sensor ring in a native structure of a membrane-embedded potassium channel.	Shi L, Zheng H, Zheng H, Borkowski BA, Shi D, Gonen T, Jiang QX.	Proc Natl Acad Sci U S A	10.1073/pnas.1218203110	2013
	X-ray structure of the fourth type of archaeal tRNA splicing endonuclease: insights into the evolution of a novel three-unit composition and a unique loop involved in broad substrate specificity.	Hirata A, Fujishima K, Yamagami R, Kawamura T, Banfield JF, Kanai A, Hori H.	Nucleic Acids Res	10.1093/nar/gks826	2012
Enzymology	Bringing Bioactive Compounds into Membranes: The UbiA Superfamily of Intramembrane Aromatic Prenyltransferases.	Li W.	Trends Biochem Sci	10.1016/j.tibs.2016.01.007	2016
	Artificial self-sufficient P450 in reversed micelles.	Hirakawa H, Kamiya N, Kawarabayasi Y, Nagamune T.	Molecules	10.3390/molecules15052935	2010
Genetics	Links from genome proteins to known 3-D structures.	Wang Y, Bryant S, Tatusov R, Tatusova T.	Genome Res	10.1101/gr.143200	2000
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	Characterisation of a synthetic Archeal membrane reveals a possible new adaptation route to extreme conditions.	Salvador-Castell M, Golub M, Erwin N, Deme B, Brooks NJ, Winter R, Peters J, Oger PM.	Commun Biol	10.1038/s42003-021-02178-y	2021
	Substrate specificity of 2-deoxy-D-ribose 5-phosphate aldolase (DERA) assessed by different protein engineering and machine learning methods.	Voutilainen S, Heinonen M, Andberg M, Jokinen E, Maaheimo H, Paakkonen J, Hakulinen N, Rouvinen J, Lahdesmaki H, Kaski S, Rousu J, Penttila M, Koivula A.	Appl Microbiol Biotechnol	10.1007/s00253-020-10960-x	2020
Metabolism	Reversible ADP-ribosylation of RNA.	Munnur D, Bartlett E, Mikolcevic P, Kirby IT, Rack JGM, Mikoc A, Cohen MS, Ahel I.	Nucleic Acids Res	10.1093/nar/gkz305	2019
	Structural basis for mRNA surveillance by archaeal Pelota and GTP-bound EF1alpha complex.	Kobayashi K, Kikuno I, Kuroha K, Saito K, Ito K, Ishitani R, Inada T, Nureki O.	Proc Natl Acad Sci U S A	10.1073/pnas.1009598107	2010
	Phylogenetic study of the evolution of PEP-carboxykinase.	Aich S, Delbaere LT.	Evol Bioinform Online		2007
Metabolism	Determining the fidelity of tRNA aminoacylation via microarrays.	Schwartz MH, Pan T.	Methods	10.1016/j.ymeth.2016.09.004	2017
	Composition bias and the origin of ORFan genes.	Yomtovian I, Teerakulkittipong N, Lee B, Moult J, Unger R.	Bioinformatics	10.1093/bioinformatics/btq093	2010
Metabolism	Effects of Low Intensity Focused Ultrasound on Liposomes Containing Channel proteins.	Babakhanian M, Yang L, Nowroozi B, Saddik G, Boodaghians L, Blount P, Grundfest W.	Sci Rep	10.1038/s41598-018-35486-1	2018
	Conversion of Mevalonate 3-Kinase into 5-Phosphomevalonate 3-Kinase by Single Amino Acid Mutations.	Motoyama K, Sobue F, Kawaide H, Yoshimura T, Hemmi H.	Appl Environ Microbiol	10.1128/aem.00256-19	2019
	Crystallization of the archaeal transcription termination factor NusA: a significant decrease in twinning under microgravity conditions.	Tanaka H, Umehara T, Inaka K, Takahashi S, Shibata R, Bessho Y, Sato M, Sugiyama S, Fusatomi E, Terada T, Shirouzu M, Sano S, Motohara M, Kobayashi T, Tanaka T, Tanaka A, Yokoyama S.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309106054625	2007
	Purification, crystallization and preliminary X-ray analysis of the PCNA2-PCNA3 complex from Sulfolobus tokodaii strain 7.	Kawai A, Higuchi S, Tsunoda M, Nakamura KT, Miyamoto S.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309109044479	2009
Enzymology	Crystal structures of Trypanosoma brucei oligopeptidase B broaden the paradigm of catalytic regulation in prolyl oligopeptidase family enzymes.	Canning P, Rea D, Morty RE, Fulop V.	PLoS One	10.1371/journal.pone.0079349	2013
Metabolism	Crystallization and preliminary X-ray analysis of PH1566, a putative ribosomal RNA-processing factor from the hyperthermophilic archaeon Pyrococcus horikoshii OT3.	Jia MZ, Ohtsuka J, Lee WC, Nagata K, Tanokura M.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309105040613	2006
Metabolism	Modeling the Thermoproteaceae RNase P RNA.	Chan PP, Brown JW, Lowe TM.	RNA Biol	10.4161/rna.21502	2012
Metabolism	A Shared Mechanism for the Folding of Voltage-Gated K⁺ Channels.	McDonald SK, Levitz TS, Valiyaveetil FI.	Biochemistry	10.1021/acs.biochem.9b00068	2019
	Pareto Optimality Explanation of the Glycolytic Alternatives in Nature.	Ng CY, Wang L, Chowdhury A, Maranas CD.	Sci Rep	10.1038/s41598-019-38836-9	2019
	Two-Dimensional Crystallization Procedure, from Protein Expression to Sample Preparation.	Kuang Q, Purhonen P, Hebert H.	Biomed Res Int	10.1155/2015/693869	2015
Enzymology	Molybdenum-containing arsenite oxidase of the chemolithoautotrophic arsenite oxidizer NT-26.	Santini JM, vanden Hoven RN.	J Bacteriol	10.1128/jb.186.6.1614-1619.2004	2004
	The Voltage-Dependent Deactivation of the KvAP Channel Involves the Breakage of Its S4 Helix.	Bignucolo O, Berneche S.	Front Mol Biosci	10.3389/fmolb.2020.00162	2020
Biotechnology	EstDZ3: A New Esterolytic Enzyme Exhibiting Remarkable Thermostability.	Zarafeta D, Szabo Z, Moschidi D, Phan H, Chrysina ED, Peng X, Ingham CJ, Kolisis FN, Skretas G.	Front Microbiol	10.3389/fmicb.2016.01779	2016
Metabolism	A Key Enzyme of the NAD⁺ Salvage Pathway in Thermus thermophilus: Characterization of Nicotinamidase and the Impact of Its Gene Deletion at High Temperatures.	Taniguchi H, Sungwallek S, Chotchuang P, Okano K, Honda K.	J Bacteriol	10.1128/jb.00359-17	2017
Metabolism	Compatible solutes of the hyperthermophile Palaeococcus ferrophilus: osmoadaptation and thermoadaptation in the order thermococcales.	Neves C, da Costa MS, Santos H.	Appl Environ Microbiol	10.1128/aem.71.12.8091-8098.2005	2005
	Tracing back variations in archaeal ESCRT-based cell division to protein domain architectures.	Frohn BP, Hartel T, Cox J, Schwille P.	PLoS One	10.1371/journal.pone.0266395	2022
Metabolism	Mapping the active site helix-to-strand conversion of CxxxxC peroxiredoxin Q enzymes.	Perkins A, Gretes MC, Nelson KJ, Poole LB, Karplus PA.	Biochemistry	10.1021/bi301017s	2012
	The Exploration of the Thermococcus barophilus Lipidome Reveals the Widest Variety of Phosphoglycolipids in Thermococcales.	Tourte M, Coffinet S, Wormer L, Lipp JS, Hinrichs KU, Oger PM.	Front Microbiol	10.3389/fmicb.2022.869479	2022
Pathogenicity	Exposure to 1-Butanol Exemplifies the Response of the Thermoacidophilic Archaeon Sulfolobus acidocaldarius to Solvent Stress.	Benninghoff JC, Kuschmierz L, Zhou X, Albersmeier A, Pham TK, Busche T, Wright PC, Kalinowski J, Makarova KS, Brasen C, Flemming HC, Wingender J, Siebers B.	Appl Environ Microbiol	10.1128/aem.02988-20	2021
	Structural Dynamics of the Paddle Motif Loop in the Activated Conformation of KvAP Voltage Sensor.	Das A, Chatterjee S, Raghuraman H.	Biophys J	10.1016/j.bpj.2019.08.017	2020
Metabolism	Metagenomes from Coastal Marine Sediments Give Insights into the Ecological Role and Cellular Features of Loki- and Thorarchaeota.	Manoharan L, Kozlowski JA, Murdoch RW, Loffler FE, Sousa FL, Schleper C.	mBio	10.1128/mbio.02039-19	2019
Phylogeny	Functional Classification of Uncultured "Candidatus Caldiarchaeum subterraneum" Using the Maple System.	Takami H, Arai W, Takemoto K, Uchiyama I, Taniguchi T.	PLoS One	10.1371/journal.pone.0132994	2015
	Sequence-Dependent T:G Base Pair Opening in DNA Double Helix Bound by Cren7, a Chromatin Protein Conserved among Crenarchaea.	Tian L, Zhang Z, Wang H, Zhao M, Dong Y, Gong Y.	PLoS One	10.1371/journal.pone.0163361	2016
	Profile structures of the voltage-sensor domain and the voltage-gated K(+)-channel vectorially oriented in a single phospholipid bilayer membrane at the solid-vapor and solid-liquid interfaces determined by x-ray interferometry.	Gupta S, Liu J, Strzalka J, Blasie JK.	Phys Rev E Stat Nonlin Soft Matter Phys	10.1103/physreve.84.031911	2011
Metabolism	A highly conserved family of domains related to the DNA-glycosylase fold helps predict multiple novel pathways for RNA modifications.	Burroughs AM, Aravind L.	RNA Biol	10.4161/rna.28302	2014
Metabolism	Evolutionary convergence and divergence in archaeal chromosomal proteins and Chromo-like domains from bacteria and eukaryotes.	Kaur G, Iyer LM, Subramanian S, Aravind L.	Sci Rep	10.1038/s41598-018-24467-z	2018
	Electrophilic activity-based RNA probes reveal a self-alkylating RNA for RNA labeling.	McDonald RI, Guilinger JP, Mukherji S, Curtis EA, Lee WI, Liu DR.	Nat Chem Biol	10.1038/nchembio.1655	2014
Phylogeny	The Medium-Chain Dehydrogenase/reductase Engineering Database: a systematic analysis of a diverse protein family to understand sequence-structure-function relationship.	Knoll M, Pleiss J.	Protein Sci	10.1110/ps.035428.108	2008
Enzymology	Expression, purification and crystallization of a thermostable short-chain alcohol dehydrogenase from the archaeon Thermococcus sibiricus.	Lyashenko AV, Bezsudnova EY, Gumerov VM, Lashkov AA, Mardanov AV, Mikhailov AM, Polyakov KM, Popov VO, Ravin NV, Skryabin KG, Zabolotniy VK, Stekhanova TN, Kovalchuk MV.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309110002654	2010
	A synthetic S6 segment derived from KvAP channel self-assembles, permeabilizes lipid vesicles, and exhibits ion channel activity in bilayer lipid membrane.	Verma R, Malik C, Azmi S, Srivastava S, Ghosh S, Ghosh JK.	J Biol Chem	10.1074/jbc.m110.209676	2011
Enzymology	NMR solution structures of Runella slithyformis RNA 2'-phosphotransferase Tpt1 provide insights into NAD+ binding and specificity.	Alphonse S, Banerjee A, Dantuluri S, Shuman S, Ghose R.	Nucleic Acids Res	10.1093/nar/gkab241	2021
	Electrostatic interaction between dipoles and side chains in the voltage sensor domain of K(+) channel.	Mapder T, Adhya S, Adhya L.	J Nat Sci Biol Med	10.4103/0976-9668.107259	2013
Metabolism	S6 peptide derived from KvAP channel shows cooperativity in gating on bilayer lipid membrane.	Malik C, Ghosh S.	PLoS One	10.1371/journal.pone.0078845	2013
Metabolism	Protein glutaminylation is a yeast-specific posttranslational modification of elongation factor 1A.	Jank T, Belyi Y, Wirth C, Rospert S, Hu Z, Dengjel J, Tzivelekidis T, Andersen GR, Hunte C, Schlosser A, Aktories K.	J Biol Chem	10.1074/jbc.m117.801035	2017
	Mining for Perchlorate Resistance Genes in Microorganisms From Sediments of a Hypersaline Pond in Atacama Desert, Chile.	Diaz-Rullo J, Rodriguez-Valdecantos G, Torres-Rojas F, Cid L, Vargas IT, Gonzalez B, Gonzalez-Pastor JE.	Front Microbiol	10.3389/fmicb.2021.723874	2021
Enzymology	Structure and catalysis of acylaminoacyl peptidase: closed and open subunits of a dimer oligopeptidase.	Harmat V, Domokos K, Menyhard DK, Pallo A, Szeltner Z, Szamosi I, Beke-Somfai T, Naray-Szabo G, Polgar L.	J Biol Chem	10.1074/jbc.m110.169862	2011
	In Staphylococcus aureus the regulation of pyruvate kinase activity by serine/threonine protein kinase favors biofilm formation.	Vasu D, Sunitha MM, Srikanth L, Swarupa V, Prasad UV, Sireesha K, Yeswanth S, Kumar PS, Venkatesh K, Chaudhary A, Sarma PV.	3 Biotech	10.1007/s13205-014-0248-3	2015
Enzymology	Viral assemblage composition in Yellowstone acidic hot springs assessed by network analysis.	Bolduc B, Wirth JF, Mazurie A, Young MJ.	ISME J	10.1038/ismej.2015.28	2015
Metabolism	A New APEH Cluster with Antioxidant Functions in the Antarctic Hemoglobinless Icefish Chionodraco hamatus.	Riccio A, Gogliettino M, Palmieri G, Balestrieri M, Facchiano A, Rossi M, Palumbo S, Monti G, Cocca E.	PLoS One	10.1371/journal.pone.0125594	2015
	The Carbon Switch at the Level of Pyruvate and Phosphoenolpyruvate in Sulfolobus solfataricus P2.	Haferkamp P, Tjaden B, Shen L, Brasen C, Kouril T, Siebers B.	Front Microbiol	10.3389/fmicb.2019.00757	2019
Metabolism	Sucrose Metabolism in Haloarchaea: Reassessment Using Genomics, Proteomics, and Metagenomics.	Williams TJ, Allen MA, Liao Y, Raftery MJ, Cavicchioli R.	Appl Environ Microbiol	10.1128/aem.02935-18	2019
Transcriptome	RIP-Seq Suggests Translational Regulation by L7Ae in Archaea.	Daume M, Uhl M, Backofen R, Randau L.	mBio	10.1128/mbio.00730-17	2017
Phylogeny	Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox.	Brochier C, Forterre P, Gribaldo S.	Genome Biol	10.1186/gb-2004-5-3-r17	2004
	Prodigal: prokaryotic gene recognition and translation initiation site identification.	Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ.	BMC Bioinformatics	10.1186/1471-2105-11-119	2010
Genetics	Evolution of DNA replication protein complexes in eukaryotes and Archaea.	Chia N, Cann I, Olsen GJ.	PLoS One	10.1371/journal.pone.0010866	2010
Enzymology	Domain cross-talk within a bifunctional enzyme provides catalytic and allosteric functionality in the biosynthesis of aromatic amino acids.	Bai Y, Lang EJM, Nazmi AR, Parker EJ.	J Biol Chem	10.1074/jbc.ra118.005220	2019
Enzymology	Minimal requirements for reverse polymerization and tRNA repair by tRNA^His guanylyltransferase.	Desai R, Kim K, Buchsenschutz HC, Chen AW, Bi Y, Mann MR, Turk MA, Chung CZ, Heinemann IU.	RNA Biol	10.1080/15476286.2017.1372076	2018
	RNA Thermodynamic Structural Entropy.	Garcia-Martin JA, Clote P.	PLoS One	10.1371/journal.pone.0137859	2015
	Crystallization and preliminary X-ray analysis of hyperthermophilic L-threonine dehydrogenase from the archaeon Pyrococcus horikoshii.	Higashi N, Matsuura T, Nakagawa A, Ishikawa K.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s174430910500881x	2005
Proteome	In vitro folding of KvAP, a voltage-gated K+ channel.	Devaraneni PK, Devereaux JJ, Valiyaveetil FI.	Biochemistry	10.1021/bi2012965	2011
Enzymology	Diversity of archaeosine synthesis in crenarchaeota.	Phillips G, Swairjo MA, Gaston KW, Bailly M, Limbach PA, Iwata-Reuyl D, de Crecy-Lagard V.	ACS Chem Biol	10.1021/cb200361w	2012
Metabolism	Duplication of leucyl-tRNA synthetase in an archaeal extremophile may play a role in adaptation to variable environmental conditions.	Weitzel CS, Li L, Zhang C, Eilts KK, Bretz NM, Gatten AL, Whitaker RJ, Martinis SA.	J Biol Chem	10.1074/jbc.ra118.006481	2020
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	Multiscale modeling shows that dielectric differences make NaV channels faster than KV channels.	Catacuzzeno L, Sforna L, Franciolini F, Eisenberg RS.	J Gen Physiol	10.1085/jgp.202012706	2021
Genetics	MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes.	Cruveiller S, Le Saux J, Vallenet D, Lajus A, Bocs S, Medigue C.	Nucleic Acids Res	10.1093/nar/gki498	2005
Metabolism	The TK0271 Protein Activates Transcription of Aromatic Amino Acid Biosynthesis Genes in the Hyperthermophilic Archaeon Thermococcus kodakarensis.	Yamamoto Y, Kanai T, Kaneseki T, Atomi H.	mBio	10.1128/mbio.01213-19	2019
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Metabolism	Opsin-Mediated Inhibition of Bacterioruberin Synthesis in Halophilic Archaea.	Peck RF, Plesa AM, Graham SM, Angelini DR, Shaw EL.	J Bacteriol	10.1128/jb.00303-17	2017
Metabolism	Interaction of diverse voltage sensor homologs with lipid bilayers revealed by self-assembly simulations.	Mokrab Y, Sansom MS.	Biophys J	10.1016/j.bpj.2010.11.049	2011
Enzymology	Structure of the archaeal pab87 peptidase reveals a novel self-compartmentalizing protease family.	Delfosse V, Girard E, Birck C, Delmarcelle M, Delarue M, Poch O, Schultz P, Mayer C.	PLoS One	10.1371/journal.pone.0004712	2009
Metabolism	CC1, a novel crenarchaeal DNA binding protein.	Luo X, Schwarz-Linek U, Botting CH, Hensel R, Siebers B, White MF.	J Bacteriol	10.1128/jb.01246-06	2007
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Metabolism	The Interaction between the Ribosomal Stalk Proteins and Translation Initiation Factor 5B Promotes Translation Initiation.	Murakami R, Singh CR, Morris J, Tang L, Harmon I, Takasu A, Miyoshi T, Ito K, Asano K, Uchiumi T.	Mol Cell Biol	10.1128/mcb.00067-18	2018
Metabolism	Discovery of widespread GTP-binding motifs in genomic DNA and RNA.	Curtis EA, Liu DR.	Chem Biol	10.1016/j.chembiol.2013.02.015	2013
Enzymology	Identification and characterisation of a novel acylpeptide hydrolase from Sulfolobus solfataricus: structural and functional insights.	Gogliettino M, Balestrieri M, Cocca E, Mucerino S, Rossi M, Petrillo M, Mazzella E, Palmieri G.	PLoS One	10.1371/journal.pone.0037921	2012
Metabolism	Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes.	Lomsadze A, Gemayel K, Tang S, Borodovsky M.	Genome Res	10.1101/gr.230615.117	2018
Enzymology	Characterization of a thermophilic ATP-dependent DNA ligase from the euryarchaeon Pyrococcus horikoshii.	Keppetipola N, Shuman S.	J Bacteriol	10.1128/jb.187.20.6902-6908.2005	2005
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Enzymology	Purification, crystallization and preliminary X-ray crystallographic study of the L-fuculose-1-phosphate aldolase (FucA) from Thermus thermophilus HB8.	Jeyakanthan J, Taka J, Kikuchi A, Kuroishi C, Yutani K, Shiro Y.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309105036766	2005
Genetics	PEDANT genome database: 10 years online.	Riley ML, Schmidt T, Artamonova II, Wagner C, Volz A, Heumann K, Mewes HW, Frishman D.	Nucleic Acids Res	10.1093/nar/gkl1005	2007
Metabolism	Unusual Phosphoenolpyruvate (PEP) Synthetase-Like Protein Crucial to Enhancement of Polyhydroxyalkanoate Accumulation in Haloferax mediterranei Revealed by Dissection of PEP-Pyruvate Interconversion Mechanism.	Chen J, Mitra R, Zhang S, Zuo Z, Lin L, Zhao D, Xiang H, Han J.	Appl Environ Microbiol	10.1128/aem.00984-19	2019
	Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1).	Goker M, Held B, Lapidus A, Nolan M, Spring S, Yasawong M, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Goodwin L, Tapia R, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Brambilla E, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Detter JC, Han C, Rohde M, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.	Stand Genomic Sci	10.4056/sigs.1072907	2010
Enzymology	Crystallization and preliminary X-ray crystallographic analysis of Sulfolobus solfataricus thioredoxin reductase.	Ruggiero A, Ruocco MR, Grimaldi P, Arcari P, Masullo M, Zagari A, Vitagliano L.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309105027995	2005
Proteome	Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches.	Knizewski L, Kinch LN, Grishin NV, Rychlewski L, Ginalski K.	BMC Struct Biol	10.1186/1472-6807-7-40	2007
Metabolism	Improving the 'tool box' for robust industrial enzymes.	Littlechild JA.	J Ind Microbiol Biotechnol	10.1007/s10295-017-1920-5	2017
Enzymology	Methods for Structural and Functional Analyses of Intramembrane Prenyltransferases in the UbiA Superfamily.	Yang Y, Ke N, Liu S, Li W.	Methods Enzymol	10.1016/bs.mie.2016.10.032	2017
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Metabolism	Assembly defects of human tRNA splicing endonuclease contribute to impaired pre-tRNA processing in pontocerebellar hypoplasia.	Sekulovski S, Devant P, Panizza S, Gogakos T, Pitiriciu A, Heitmeier K, Ramsay EP, Barth M, Schmidt C, Tuschl T, Baas F, Weitzer S, Martinez J, Trowitzsch S.	Nat Commun	10.1038/s41467-021-25870-3	2021
Metabolism	Thermostable alcohol dehydrogenase from Thermococcus kodakarensis KOD1 for enantioselective bioconversion of aromatic secondary alcohols.	Wu X, Zhang C, Orita I, Imanaka T, Fukui T, Xing XH.	Appl Environ Microbiol	10.1128/aem.03873-12	2013
Metabolism	Unusual Butane- and Pentanetriol-Based Tetraether Lipids in Methanomassiliicoccus luminyensis, a Representative of the Seventh Order of Methanogens.	Becker KW, Elling FJ, Yoshinaga MY, Sollinger A, Urich T, Hinrichs KU.	Appl Environ Microbiol	10.1128/aem.00772-16	2016
Genetics	Diversity and evolution of multiple orc/cdc6-adjacent replication origins in haloarchaea.	Wu Z, Liu H, Liu J, Liu X, Xiang H.	BMC Genomics	10.1186/1471-2164-13-478	2012
Enzymology	Two family B DNA polymerases from Aeropyrum pernix, an aerobic hyperthermophilic crenarchaeote.	Cann IK, Ishino S, Nomura N, Sako Y, Ishino Y.	J Bacteriol	10.1128/jb.181.19.5984-5992.1999	1999
Enzymology	NurA, a novel 5'-3' nuclease gene linked to rad50 and mre11 homologs of thermophilic Archaea.	Constantinesco F, Forterre P, Elie C.	EMBO Rep	10.1093/embo-reports/kvf112	2002
Metabolism	Archaea recruited D-Tyr-tRNATyr deacylase for editing in Thr-tRNA synthetase.	Rigden DJ.	RNA	10.1261/rna.7115404	2004
Enzymology	X-ray structure and characterization of carbamate kinase from the human parasite Giardia lamblia.	Galkin A, Kulakova L, Wu R, Nash TE, Dunaway-Mariano D, Herzberg O.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309110004665	2010
Metabolism	Purification, crystallization and preliminary crystallographic analysis of protein MJ1225 from Methanocaldococcus jannaschii, a putative archaeal homologue of gamma-AMPK.	Gomez Garcia I, Kortazar D, Oyenarte I, Mato JM, Martinez-Chantar ML, Martinez-Cruz LA.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309109026475	2009
Enzymology	Crystallization and preliminary X-ray diffraction studies of an alcohol dehydrogenase from the Antarctic psychrophile Moraxella sp. TAE123.	Papanikolau Y, Tsigos I, Papadovasilaki M, Bouriotis V, Petratos K.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309105002253	2005
Metabolism	The molecular structure of Schistosoma mansoni PNP isoform 2 provides insights into the nucleoside selectivity of PNPs.	Torini JR, Romanello L, Batista FAH, Serrao VHB, Faheem M, Zeraik AE, Bird L, Nettleship J, Reddivari Y, Owens R, DeMarco R, Borges JC, Brandao-Neto J, Pereira HD.	PLoS One	10.1371/journal.pone.0203532	2018
Metabolism	Conditional accumulation of toxic tRNAs to cause amino acid misincorporation.	Zimmerman SM, Kon Y, Hauke AC, Ruiz BY, Fields S, Phizicky EM.	Nucleic Acids Res	10.1093/nar/gky623	2018
Metabolism	High yield purification of full-length functional hERG K+ channels produced in Saccharomyces cerevisiae.	Molbaek K, Scharff-Poulsen P, Helix-Nielsen C, Klaerke DA, Pedersen PA.	Microb Cell Fact	10.1186/s12934-015-0193-9	2015
	Differential Subcellular Localization of Leishmania Alba-Domain Proteins throughout the Parasite Development.	Dupe A, Dumas C, Papadopoulou B.	PLoS One	10.1371/journal.pone.0137243	2015
	Predicting candidate genomic sequences that correspond to synthetic functional RNA motifs.	Laserson U, Gan HH, Schlick T.	Nucleic Acids Res	10.1093/nar/gki911	2005
Metabolism	Role of alcohols in growth, lipid composition, and membrane fluidity of yeasts, bacteria, and archaea.	Huffer S, Clark ME, Ning JC, Blanch HW, Clark DS.	Appl Environ Microbiol	10.1128/aem.00694-11	2011
Proteome	The sensitive balance between the fully folded and locally unfolded conformations of a model peroxiredoxin.	Perkins A, Nelson KJ, Williams JR, Parsonage D, Poole LB, Karplus PA.	Biochemistry	10.1021/bi4011573	2013
Genetics	Insights and inferences about integron evolution from genomic data.	Nemergut DR, Robeson MS, Kysela RF, Martin AP, Schmidt SK, Knight R.	BMC Genomics	10.1186/1471-2164-9-261	2008
Metabolism	Structural basis of lipid-driven conformational transitions in the KvAP voltage-sensing domain.	Li Q, Wanderling S, Sompornpisut P, Perozo E.	Nat Struct Mol Biol	10.1038/nsmb.2747	2014
Metabolism	Specificity and function of archaeal DNA replication initiator proteins.	Samson RY, Xu Y, Gadelha C, Stone TA, Faqiri JN, Li D, Qin N, Pu F, Liang YX, She Q, Bell SD.	Cell Rep	10.1016/j.celrep.2013.01.002	2013
	Start Codon Recognition in Eukaryotic and Archaeal Translation Initiation: A Common Structural Core.	Schmitt E, Coureux PD, Monestier A, Dubiez E, Mechulam Y.	Int J Mol Sci	10.3390/ijms20040939	2019
Metabolism	Characterization of the replication initiator Orc1/Cdc6 from the Archaeon Picrophilus torridus.	Arora J, Goswami K, Saha S.	J Bacteriol	10.1128/jb.01020-13	2014
Metabolism	Artificial modulation of the gating behavior of a K+ channel in a KvAP-DNA chimera.	Wang A, Zocchi G.	PLoS One	10.1371/journal.pone.0018598	2011
Genetics	Comparative genomics reveals conserved positioning of essential genomic clusters in highly rearranged Thermococcales chromosomes.	Cossu M, Da Cunha V, Toffano-Nioche C, Forterre P, Oberto J.	Biochimie	10.1016/j.biochi.2015.07.008	2015
	In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs.	Sugahara J, Yachie N, Arakawa K, Tomita M.	RNA	10.1261/rna.309507	2007
Enzymology	Biochemical properties and regulated gene expression of the superoxide dismutase from the facultatively aerobic hyperthermophile Pyrobaculum calidifontis.	Amo T, Atomi H, Imanaka T.	J Bacteriol	10.1128/jb.185.21.6340-6347.2003	2003
Enzymology	Biochemical characterisation of LigN, an NAD+-dependent DNA ligase from the halophilic euryarchaeon Haloferax volcanii that displays maximal in vitro activity at high salt concentrations.	Poidevin L, MacNeill SA.	BMC Mol Biol	10.1186/1471-2199-7-44	2006
Enzymology	Peroxiredoxin Catalysis at Atomic Resolution.	Perkins A, Parsonage D, Nelson KJ, Ogba OM, Cheong PH, Poole LB, Karplus PA.	Structure	10.1016/j.str.2016.07.012	2016
	Significance of two distinct types of tryptophan synthase beta chain in Bacteria, Archaea and higher plants.	Xie G, Forst C, Bonner C, Jensen RA.	Genome Biol	10.1186/gb-2001-3-1-research0004	2002
	The Proteome and Lipidome of Thermococcus kodakarensis across the Stationary Phase.	Gagen EJ, Yoshinaga MY, Garcia Prado F, Hinrichs KU, Thomm M.	Archaea	10.1155/2016/5938289	2016
Metabolism	Cryo-EM structures of the XPF-ERCC1 endonuclease reveal how DNA-junction engagement disrupts an auto-inhibited conformation.	Jones M, Beuron F, Borg A, Nans A, Earl CP, Briggs DC, Snijders AP, Bowles M, Morris EP, Linch M, McDonald NQ.	Nat Commun	10.1038/s41467-020-14856-2	2020
Metabolism	TOR regulates the subcellular distribution of DIM2, a KH domain protein required for cotranscriptional ribosome assembly and pre-40S ribosome export.	Vanrobays E, Leplus A, Osheim YN, Beyer AL, Wacheul L, Lafontaine DL.	RNA	10.1261/rna.1176708	2008
Metabolism	(ADP-ribosyl)hydrolases: structure, function, and biology.	Rack JGM, Palazzo L, Ahel I.	Genes Dev	10.1101/gad.334631.119	2020
	Biological Membranes in Extreme Conditions: Simulations of Anionic Archaeal Tetraether Lipid Membranes.	Pineda De Castro LF, Dopson M, Friedman R.	PLoS One	10.1371/journal.pone.0155287	2016
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	Evolutionary Steps in the Emergence of Life Deduced from the Bottom-Up Approach and GADV Hypothesis (Top-Down Approach).	Ikehara K.	Life (Basel)	10.3390/life6010006	2016
Enzymology	Carboxypeptidase in prolyl oligopeptidase family: Unique enzyme activation and substrate-screening mechanisms.	Yadav P, Goyal VD, Gaur NK, Kumar A, Gokhale SM, Jamdar SN, Makde RD.	J Biol Chem	10.1074/jbc.ra118.004254	2019
Metabolism	Hierarchical modularity of nested bow-ties in metabolic networks.	Zhao J, Yu H, Luo JH, Cao ZW, Li YX.	BMC Bioinformatics	10.1186/1471-2105-7-386	2006
Enzymology	The small subunit AroB of arsenite oxidase: lessons on the [2Fe-2S] Rieske protein superfamily.	Duval S, Santini JM, Nitschke W, Hille R, Schoepp-Cothenet B.	J Biol Chem	10.1074/jbc.m110.113811	2010
	Analysis of the peroxiredoxin family: using active-site structure and sequence information for global classification and residue analysis.	Nelson KJ, Knutson ST, Soito L, Klomsiri C, Poole LB, Fetrow JS.	Proteins	10.1002/prot.22936	2011
	Preferred and avoided codon pairs in three domains of life.	Tats A, Tenson T, Remm M.	BMC Genomics	10.1186/1471-2164-9-463	2008
Metabolism	Structure-function analysis of the yeast NAD+-dependent tRNA 2'-phosphotransferase Tpt1.	Sawaya R, Schwer B, Shuman S.	RNA	10.1261/rna.7193705	2005
Metabolism	Calcium-driven DNA synthesis by a high-fidelity DNA polymerase.	Ralec C, Henry E, Lemor M, Killelea T, Henneke G.	Nucleic Acids Res	10.1093/nar/gkx927	2017
Metabolism	Cysteine biosynthesis in Trichomonas vaginalis involves cysteine synthase utilizing O-phosphoserine.	Westrop GD, Goodall G, Mottram JC, Coombs GH.	J Biol Chem	10.1074/jbc.m600688200	2006
Metabolism	Three proliferating cell nuclear antigen-like proteins found in the hyperthermophilic archaeon Aeropyrum pernix: interactions with the two DNA polymerases.	Daimon K, Kawarabayasi Y, Kikuchi H, Sako Y, Ishino Y.	J Bacteriol	10.1128/jb.184.3.687-694.2002	2002
	The Bet v 1 fold: an ancient, versatile scaffold for binding of large, hydrophobic ligands.	Radauer C, Lackner P, Breiteneder H.	BMC Evol Biol	10.1186/1471-2148-8-286	2008
Metabolism	Single-stranded DNA Binding by the Helix-Hairpin-Helix Domain of XPF Protein Contributes to the Substrate Specificity of the ERCC1-XPF Protein Complex.	Das D, Faridounnia M, Kovacic L, Kaptein R, Boelens R, Folkers GE.	J Biol Chem	10.1074/jbc.m116.747857	2017
Enzymology	Expression, purification, crystallization and preliminary X-ray analysis of a nucleoside kinase from the hyperthermophile Methanocaldococcus jannaschii.	Arnfors L, Hansen T, Meining W, Schonheit P, Ladenstein R.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309105015642	2005
Metabolism	TMEM266 is a functional voltage sensor regulated by extracellular Zn².	Papp F, Lomash S, Szilagyi O, Babikow E, Smith J, Chang TH, Bahamonde MI, Toombes GES, Swartz KJ.	Elife	10.7554/elife.42372	2019
	Functional relevance of dynamic properties of Dimeric NADP-dependent Isocitrate Dehydrogenases.	Vinekar R, Verma C, Ghosh I.	BMC Bioinformatics	10.1186/1471-2105-13-s17-s2	2012
Metabolism	Yeast mitochondrial threonyl-tRNA synthetase recognizes tRNA isoacceptors by distinct mechanisms and promotes CUN codon reassignment.	Ling J, Peterson KM, Simonovic I, Cho C, Soll D, Simonovic M.	Proc Natl Acad Sci U S A	10.1073/pnas.1200109109	2012
Enzymology	Bifunctional CTP:inositol-1-phosphate cytidylyltransferase/CDP-inositol:inositol-1-phosphate transferase, the key enzyme for di-myo-inositol-phosphate synthesis in several (hyper)thermophiles.	Rodrigues MV, Borges N, Henriques M, Lamosa P, Ventura R, Fernandes C, Empadinhas N, Maycock C, da Costa MS, Santos H.	J Bacteriol	10.1128/jb.00465-07	2007
	Molecular template for a voltage sensor in a novel K+ channel. I. Identification and functional characterization of KvLm, a voltage-gated K+ channel from Listeria monocytogenes.	Santos JS, Lundby A, Zazueta C, Montal M.	J Gen Physiol	10.1085/jgp.200609572	2006
	Molecular characterization and postsplicing fate of three introns within the single rRNA operon of the hyperthermophilic archaeon Aeropyrum pernix K1.	Nomura N, Sako Y, Uchida A.	J Bacteriol	10.1128/jb.180.14.3635-3643.1998	1998
	Kinetic analysis of the interactions between plant thioredoxin and target proteins.	Hara S, Hisabori T.	Front Plant Sci	10.3389/fpls.2013.00508	2013
Metabolism	Crystal structure of mammalian selenocysteine-dependent iodothyronine deiodinase suggests a peroxiredoxin-like catalytic mechanism.	Schweizer U, Schlicker C, Braun D, Kohrle J, Steegborn C.	Proc Natl Acad Sci U S A	10.1073/pnas.1323873111	2014
Metabolism	Biosynthesis and trafficking of heme o and heme a: new structural insights and their implications for reaction mechanisms and prenylated heme transfer.	Rivett ED, Heo L, Feig M, Hegg EL.	Crit Rev Biochem Mol Biol	10.1080/10409238.2021.1957668	2021
Genetics	Trypanosome prereplication machinery contains a single functional orc1/cdc6 protein, which is typical of archaea.	Godoy PD, Nogueira-Junior LA, Paes LS, Cornejo A, Martins RM, Silber AM, Schenkman S, Elias MC.	Eukaryot Cell	10.1128/ec.00161-09	2009
Metabolism	A bifunctional archaeal protein that is a component of 30S ribosomal subunits and interacts with C/D box small RNAs.	Ciammaruconi A, Gorini S, Londei P.	Archaea	10.1155/2008/472786	2008
	Engineering of the Hyperthermophilic Archaeon Thermococcus kodakarensis for Chitin-Dependent Hydrogen Production.	Aslam M, Horiuchi A, Simons JR, Jha S, Yamada M, Odani T, Fujimoto R, Yamamoto Y, Gunji R, Imanaka T, Kanai T, Atomi H.	Appl Environ Microbiol	10.1128/aem.00280-17	2017
Genetics	Identification of genomic features using microsyntenies of domains: domain teams.	Pasek S, Bergeron A, Risler JL, Louis A, Ollivier E, Raffinot M.	Genome Res	10.1101/gr.3638405	2005
Metabolism	A novel pathway for the biosynthesis of heme in Archaea: genome-based bioinformatic predictions and experimental evidence.	Storbeck S, Rolfes S, Raux-Deery E, Warren MJ, Jahn D, Layer G.	Archaea	10.1155/2010/175050	2010
	COPS--a novel workbench for explorations in fold space.	Suhrer SJ, Wiederstein M, Gruber M, Sippl MJ.	Nucleic Acids Res	10.1093/nar/gkp411	2009
Lipids	The catalytic and structural basis of archaeal glycerophospholipid biosynthesis.	de Kok NAW, Driessen AJM.	Extremophiles	10.1007/s00792-022-01277-w	2022
	How Diverse Are the Protein-Bound Conformations of Small-Molecule Drugs and Cofactors?	Friedrich NO, Simsir M, Kirchmair J.	Front Chem	10.3389/fchem.2018.00068	2018
Genetics	Congruent evolution of different classes of non-coding DNA in prokaryotic genomes.	Rogozin IB, Makarova KS, Natale DA, Spiridonov AN, Tatusov RL, Wolf YI, Yin J, Koonin EV.	Nucleic Acids Res	10.1093/nar/gkf549	2002
Metabolism	Pyrobaculum yellowstonensis Strain WP30 Respires on Elemental Sulfur and/or Arsenate in Circumneutral Sulfidic Geothermal Sediments of Yellowstone National Park.	Jay ZJ, Beam JP, Dohnalkova A, Lohmayer R, Bodle B, Planer-Friedrich B, Romine M, Inskeep WP.	Appl Environ Microbiol	10.1128/aem.01095-15	2015
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Metabolism	Methanocaldococcus jannaschii uses a modified mevalonate pathway for biosynthesis of isopentenyl diphosphate.	Grochowski LL, Xu H, White RH.	J Bacteriol	10.1128/jb.188.9.3192-3198.2006	2006
	Adaptations of archaeal and bacterial membranes to variations in temperature, pH and pressure.	Siliakus MF, van der Oost J, Kengen SWM.	Extremophiles	10.1007/s00792-017-0939-x	2017
Enzymology	Activation of a chimeric Rpb5/RpoH subunit using library selection.	Sommer B, Waege I, Pollmann D, Seitz T, Thomm M, Sterner R, Hausner W.	PLoS One	10.1371/journal.pone.0087485	2014
Enzymology	An antioxidant response is involved in resistance of Giardia duodenalis to albendazole.	Arguello-Garcia R, Cruz-Soto M, Gonzalez-Trejo R, Paz-Maldonado LM, Bazan-Tejeda ML, Mendoza-Hernandez G, Ortega-Pierres G.	Front Microbiol	10.3389/fmicb.2015.00286	2015
	Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds.	Mallick P, Boutz DR, Eisenberg D, Yeates TO.	Proc Natl Acad Sci U S A	10.1073/pnas.142310499	2002
	A computational method to predict genetically encoded rare amino acids in proteins.	Chaudhuri BN, Yeates TO.	Genome Biol	10.1186/gb-2005-6-9-r79	2005
	Comparative study of the extracellular proteome of Sulfolobus species reveals limited secretion.	Ellen AF, Albers SV, Driessen AJ.	Extremophiles	10.1007/s00792-009-0290-y	2010
Metabolism	Identification and characterization of bifunctional proline racemase/hydroxyproline epimerase from archaea: discrimination of substrates and molecular evolution.	Watanabe S, Tanimoto Y, Nishiwaki H, Watanabe Y.	PLoS One	10.1371/journal.pone.0120349	2015
Genetics	Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs).	Natale DA, Shankavaram UT, Galperin MY, Wolf YI, Aravind L, Koonin EV.	Genome Biol	10.1186/gb-2000-1-5-research0009	2000
Metabolism	Phylophenetic properties of metabolic pathway topologies as revealed by global analysis.	Zhang Y, Li S, Skogerbo G, Zhang Z, Zhu X, Zhang Z, Sun S, Lu H, Shi B, Chen R.	BMC Bioinformatics	10.1186/1471-2105-7-252	2006
	Sequence and structural evolution of the KsgA/Dim1 methyltransferase family.	O'Farrell HC, Xu Z, Culver GM, Rife JP.	BMC Res Notes	10.1186/1756-0500-1-108	2008
Enzymology	Characterization of bioaerosols from dairy barns: reconstructing the puzzle of occupational respiratory diseases by using molecular approaches.	Blais Lecours P, Veillette M, Marsolais D, Duchaine C.	Appl Environ Microbiol	10.1128/aem.07661-11	2012
Metabolism	Biosynthesis of ribose-5-phosphate and erythrose-4-phosphate in archaea: a phylogenetic analysis of archaeal genomes.	Soderberg T.	Archaea	10.1155/2005/314760	2005
	The intrinsic flexibility of the Kv voltage sensor and its implications for channel gating.	Sands ZA, Grottesi A, Sansom MS.	Biophys J	10.1529/biophysj.105.072199	2006
Metabolism	The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota.	Anderson IJ, Dharmarajan L, Rodriguez J, Hooper S, Porat I, Ulrich LE, Elkins JG, Mavromatis K, Sun H, Land M, Lapidus A, Lucas S, Barry K, Huber H, Zhulin IB, Whitman WB, Mukhopadhyay B, Woese C, Bristow J, Kyrpides N.	BMC Genomics	10.1186/1471-2164-10-145	2009
Metabolism	Augmenting the genetic toolbox for Sulfolobus islandicus with a stringent positive selectable marker for agmatine prototrophy.	Zhang C, Cooper TE, Krause DJ, Whitaker RJ.	Appl Environ Microbiol	10.1128/aem.01608-13	2013
Genetics	Association between the dynamics of multiple replication origins and the evolution of multireplicon genome architecture in haloarchaea.	Wu Z, Yang H, Liu J, Wang L, Xiang H.	Genome Biol Evol	10.1093/gbe/evu219	2014
Metabolism	Conserved active site cysteine residue of archaeal THI4 homolog is essential for thiamine biosynthesis in Haloferax volcanii.	Hwang S, Cordova B, Chavarria N, Elbanna D, McHugh S, Rojas J, Pfeiffer F, Maupin-Furlow JA.	BMC Microbiol	10.1186/s12866-014-0260-0	2014
Metabolism	The Tomato Nucleotide-binding Leucine-rich Repeat Immune Receptor I-2 Couples DNA-binding to Nucleotide-binding Domain Nucleotide Exchange.	Fenyk S, Dixon CH, Gittens WH, Townsend PD, Sharples GJ, Palsson LO, Takken FL, Cann MJ.	J Biol Chem	10.1074/jbc.m115.698589	2016
	Structural basis for translation termination by archaeal RF1 and GTP-bound EF1alpha complex.	Kobayashi K, Saito K, Ishitani R, Ito K, Nureki O.	Nucleic Acids Res	10.1093/nar/gks660	2012
	Crystal structures and molecular dynamics simulations of thermophilic malate dehydrogenase reveal critical loop motion for co-substrate binding.	Hung CH, Hwang TS, Chang YY, Luo HR, Wu SP, Hsu CH.	PLoS One	10.1371/journal.pone.0083091	2013
	Exclusive use of trans-editing domains prevents proline mistranslation.	Vargas-Rodriguez O, Musier-Forsyth K.	J Biol Chem	10.1074/jbc.m113.467795	2013
Metabolism	Molecular phylogeny and intricate evolutionary history of the three isofunctional enzymes involved in the oxidation of protoporphyrinogen IX.	Kobayashi K, Masuda T, Tajima N, Wada H, Sato N.	Genome Biol Evol	10.1093/gbe/evu170	2014
Metabolism	A green fluorescent protein screen for identification of well-expressed membrane proteins from a cohort of extremophilic organisms.	Hammon J, Palanivelu DV, Chen J, Patel C, Minor DL.	Protein Sci	10.1002/pro.18	2009
Metabolism	Portability of paddle motif function and pharmacology in voltage sensors.	Alabi AA, Bahamonde MI, Jung HJ, Kim JI, Swartz KJ.	Nature	10.1038/nature06266	2007
Enzymology	The phosphoenolpyruvate carboxylase from Methanothermobacter thermautotrophicus has a novel structure.	Patel HM, Kraszewski JL, Mukhopadhyay B.	J Bacteriol	10.1128/jb.186.15.5129-5137.2004	2004
Metabolism	Functional analysis of the validamycin biosynthetic gene cluster and engineered production of validoxylamine A.	Bai L, Li L, Xu H, Minagawa K, Yu Y, Zhang Y, Zhou X, Floss HG, Mahmud T, Deng Z.	Chem Biol	10.1016/j.chembiol.2006.02.002	2006
Stress	Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function.	Inskeep WP, Rusch DB, Jay ZJ, Herrgard MJ, Kozubal MA, Richardson TH, Macur RE, Hamamura N, Jennings Rd, Fouke BW, Reysenbach AL, Roberto F, Young M, Schwartz A, Boyd ES, Badger JH, Mathur EJ, Ortmann AC, Bateson M, Geesey G, Frazier M.	PLoS One	10.1371/journal.pone.0009773	2010
	SORGOdb: Superoxide Reductase Gene Ontology curated DataBase.	Lucchetti-Miganeh C, Goudenege D, Thybert D, Salbert G, Barloy-Hubler F.	BMC Microbiol	10.1186/1471-2180-11-105	2011
	Rigorous performance evaluation in protein structure modelling and implications for computational biology.	Moult J.	Philos Trans R Soc Lond B Biol Sci	10.1098/rstb.2005.1810	2006
Enzymology	Unique presence of a manganese catalase in a hyperthermophilic archaeon, Pyrobaculum calidifontis VA1.	Amo T, Atomi H, Imanaka T.	J Bacteriol	10.1128/jb.184.12.3305-3312.2002	2002
Metabolism	CysK2 from Mycobacterium tuberculosis is an O-phospho-L-serine-dependent S-sulfocysteine synthase.	Steiner EM, Both D, Lossl P, Vilaplana F, Schnell R, Schneider G.	J Bacteriol	10.1128/jb.01851-14	2014
	Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties.	Boekhorst J, Snel B.	BMC Bioinformatics	10.1186/1471-2105-8-356	2007
Genetics	Evolutionary analysis by whole-genome comparisons.	Bansal AK, Meyer TE.	J Bacteriol	10.1128/jb.184.8.2260-2272.2002	2002
Metabolism	Transcriptomes of the Extremely Thermoacidophilic Archaeon Metallosphaera sedula Exposed to Metal "Shock" Reveal Generic and Specific Metal Responses.	Wheaton GH, Mukherjee A, Kelly RM.	Appl Environ Microbiol	10.1128/aem.01176-16	2016
Metabolism	Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme.	Ahmad S, Muthukumar S, Kuncha SK, Routh SB, Yerabham AS, Hussain T, Kamarthapu V, Kruparani SP, Sankaranarayanan R.	Nat Commun	10.1038/ncomms8552	2015
Metabolism	Sulfolobus replication factor C stimulates the activity of DNA polymerase B1.	Xing X, Zhang L, Guo L, She Q, Huang L.	J Bacteriol	10.1128/jb.01552-14	2014
	Entrapment of DNA in an intersubunit tunnel system of a single-stranded DNA-binding protein.	Ghalei H, von Moeller H, Eppers D, Sohmen D, Wilson DN, Loll B, Wahl MC.	Nucleic Acids Res	10.1093/nar/gku259	2014
Genetics	Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach.	Koonin EV, Wolf YI, Aravind L.	Genome Res	10.1101/gr.162001	2001
Metabolism	A tale of two oxidation states: bacterial colonization of arsenic-rich environments.	Muller D, Medigue C, Koechler S, Barbe V, Barakat M, Talla E, Bonnefoy V, Krin E, Arsene-Ploetze F, Carapito C, Chandler M, Cournoyer B, Cruveiller S, Dossat C, Duval S, Heymann M, Leize E, Lieutaud A, Lievremont D, Makita Y, Mangenot S, Nitschke W, Ortet P, Perdrial N, Schoepp B, Siguier P, Simeonova DD, Rouy Z, Segurens B, Turlin E, Vallenet D, Van Dorsselaer A, Weiss S, Weissenbach J, Lett MC, Danchin A, Bertin PN.	PLoS Genet	10.1371/journal.pgen.0030053	2007
Phylogeny	Phylogenomics of the archaeal flagellum: rare horizontal gene transfer in a unique motility structure.	Desmond E, Brochier-Armanet C, Gribaldo S.	BMC Evol Biol	10.1186/1471-2148-7-106	2007
	Insight into the proteome of the hyperthermophilic Crenarchaeon Ignicoccus hospitalis: the major cytosolic and membrane proteins.	Burghardt T, Saller M, Gurster S, Muller D, Meyer C, Jahn U, Hochmuth E, Deutzmann R, Siedler F, Babinger P, Wirth R, Huber H, Rachel R.	Arch Microbiol	10.1007/s00203-008-0399-x	2008
Metabolism	Structure and hydration of membranes embedded with voltage-sensing domains.	Krepkiy D, Mihailescu M, Freites JA, Schow EV, Worcester DL, Gawrisch K, Tobias DJ, White SH, Swartz KJ.	Nature	10.1038/nature08542	2009
	Proliferating cell nuclear antigen restores the enzymatic activity of a DNA ligase I deficient in DNA binding.	Trasvina-Arenas CH, Cardona-Felix CS, Azuara-Liceaga E, Diaz-Quezada C, Brieba LG.	FEBS Open Bio	10.1002/2211-5463.12209	2017
Metabolism	Structure, function, and evolution of the tRNA endonucleases of Archaea: an example of subfunctionalization.	Tocchini-Valentini GD, Fruscoloni P, Tocchini-Valentini GP.	Proc Natl Acad Sci U S A	10.1073/pnas.0502350102	2005
Metabolism	Microbial K+ channels.	Loukin SH, Kuo MM, Zhou XL, Haynes WJ, Kung C, Saimi Y.	J Gen Physiol	10.1085/jgp.200509261	2005
Metabolism	Crystal structures of the kinase domain of the sulfate-activating complex in Mycobacterium tuberculosis.	Poyraz O, Brunner K, Lohkamp B, Axelsson H, Hammarstrom LG, Schnell R, Schneider G.	PLoS One	10.1371/journal.pone.0121494	2015
Metabolism	Archaeal ubiquitin-like proteins: functional versatility and putative ancestral involvement in tRNA modification revealed by comparative genomic analysis.	Makarova KS, Koonin EV.	Archaea	10.1155/2010/710303	2010
Enzymology	First characterization of an archaeal GTP-dependent phosphoenolpyruvate carboxykinase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1.	Fukuda W, Fukui T, Atomi H, Imanaka T.	J Bacteriol	10.1128/jb.186.14.4620-4627.2004	2004
	The evolutionary and functional diversity of classical and lesser-known cytoplasmic and organellar translational GTPases across the tree of life.	Atkinson GC.	BMC Genomics	10.1186/s12864-015-1289-7	2015
Metabolism	A study on the interaction of rhodamine B with methylthioadenosine phosphorylase protein sourced from an Antarctic soil metagenomic library.	Bartasun P, Cieslinski H, Bujacz A, Wierzbicka-Wos A, Kur J.	PLoS One	10.1371/journal.pone.0055697	2013
	Reconstitution of a transmembrane protein, the voltage-gated ion channel, KvAP, into giant unilamellar vesicles for microscopy and patch clamp studies.	Garten M, Aimon S, Bassereau P, Toombes GE.	J Vis Exp	10.3791/52281	2015
Metabolism	The genome of Rhodobacter sphaeroides strain 2.4.1 encodes functional cobinamide salvaging systems of archaeal and bacterial origins.	Gray MJ, Tavares NK, Escalante-Semerena JC.	Mol Microbiol	10.1111/j.1365-2958.2008.06437.x	2008
	Isozyme-specific ligands for O-acetylserine sulfhydrylase, a novel antibiotic target.	Spyrakis F, Singh R, Cozzini P, Campanini B, Salsi E, Felici P, Raboni S, Benedetti P, Cruciani G, Kellogg GE, Cook PF, Mozzarelli A.	PLoS One	10.1371/journal.pone.0077558	2013
Enzymology	Crystal structure of tetrameric homoisocitrate dehydrogenase from an extreme thermophile, Thermus thermophilus: involvement of hydrophobic dimer-dimer interaction in extremely high thermotolerance.	Miyazaki J, Asada K, Fushinobu S, Kuzuyama T, Nishiyama M.	J Bacteriol	10.1128/jb.187.19.6779-6788.2005	2005
Enzymology	Deficiency of the tRNATyr:Psi 35-synthase aPus7 in Archaea of the Sulfolobales order might be rescued by the H/ACA sRNA-guided machinery.	Muller S, Urban A, Hecker A, Leclerc F, Branlant C, Motorin Y.	Nucleic Acids Res	10.1093/nar/gkn1037	2009
Metabolism	A Porphyromonas gingivalis Periplasmic Novel Exopeptidase, Acylpeptidyl Oligopeptidase, Releases N-Acylated Di- and Tripeptides from Oligopeptides.	Nemoto TK, Ohara-Nemoto Y, Bezerra GA, Shimoyama Y, Kimura S.	J Biol Chem	10.1074/jbc.m115.687566	2016
Enzymology	Cloning and characterization of archaeal type I signal peptidase from Methanococcus voltae.	Ng SY, Jarrell KF.	J Bacteriol	10.1128/jb.185.20.5936-5942.2003	2003
Metabolism	Discovery of Pyrobaculum small RNA families with atypical pseudouridine guide RNA features.	Bernick DL, Dennis PP, Hochsmann M, Lowe TM.	RNA	10.1261/rna.031385.111	2012
	Structural insights into the functions of the FANCM-FAAP24 complex in DNA repair.	Yang H, Zhang T, Tao Y, Wang F, Tong L, Ding J.	Nucleic Acids Res	10.1093/nar/gkt788	2013
	Structural and functional insights into the DNA replication factor Cdc45 reveal an evolutionary relationship to the DHH family of phosphoesterases.	Krastanova I, Sannino V, Amenitsch H, Gileadi O, Pisani FM, Onesti S.	J Biol Chem	10.1074/jbc.m111.285395	2012
	Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers.	Brochier-Armanet C, Forterre P.	Archaea	10.1155/2006/582916	2007
Enzymology	Distribution and phylogenies of enzymes of the Embden-Meyerhof-Parnas pathway from archaea and hyperthermophilic bacteria support a gluconeogenic origin of metabolism.	Ronimus RS, Morgan HW.	Archaea	10.1155/2003/162593	2003
Genetics	Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes.	Makarova KS, Wolf YI, Forterre P, Prangishvili D, Krupovic M, Koonin EV.	Extremophiles	10.1007/s00792-014-0672-7	2014
	Structure of a membrane-embedded prenyltransferase homologous to UBIAD1.	Huang H, Levin EJ, Liu S, Bai Y, Lockless SW, Zhou M.	PLoS Biol	10.1371/journal.pbio.1001911	2014
Genetics	Proteome driven re-evaluation and functional annotation of the Streptococcus pyogenes SF370 genome.	Okamoto A, Yamada K.	BMC Microbiol	10.1186/1471-2180-11-249	2011
Metabolism	Morphology, biophysical properties and protein-mediated fusion of archaeosomes.	Sustar V, Zelko J, Lopalco P, Lobasso S, Ota A, Poklar Ulrih N, Corcelli A, Kralj-Iglic V.	PLoS One	10.1371/journal.pone.0039401	2012
	Genomic DNA k-mer spectra: models and modalities.	Chor B, Horn D, Goldman N, Levy Y, Massingham T.	Genome Biol	10.1186/gb-2009-10-10-r108	2009
Metabolism	Voltage-gated sodium channel (NaV) protein dissection creates a set of functional pore-only proteins.	Shaya D, Kreir M, Robbins RA, Wong S, Hammon J, Bruggemann A, Minor DL.	Proc Natl Acad Sci U S A	10.1073/pnas.1106811108	2011
Enzymology	A broad specificity nucleoside kinase from Thermoplasma acidophilum.	Elkin SR, Kumar A, Price CW, Columbus L.	Proteins	10.1002/prot.24212	2013
	Archaeal transcription: function of an alternative transcription factor B from Pyrococcus furiosus.	Micorescu M, Grunberg S, Franke A, Cramer P, Thomm M, Bartlett M.	J Bacteriol	10.1128/jb.01498-07	2008
Metabolism	The Mus81-Mms4 structure-selective endonuclease requires nicked DNA junctions to undergo conformational changes and bend its DNA substrates for cleavage.	Mukherjee S, Wright WD, Ehmsen KT, Heyer WD.	Nucleic Acids Res	10.1093/nar/gku265	2014
Metabolism	Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis.	Gao B, Gupta RS.	BMC Genomics	10.1186/1471-2164-8-86	2007
	Cytochromes c in Archaea: distribution, maturation, cell architecture, and the special case of Ignicoccus hospitalis.	Kletzin A, Heimerl T, Flechsler J, van Niftrik L, Rachel R, Klingl A.	Front Microbiol	10.3389/fmicb.2015.00439	2015
	Solution structure and phospholipid interactions of the isolated voltage-sensor domain from KvAP.	Butterwick JA, MacKinnon R.	J Mol Biol	10.1016/j.jmb.2010.09.012	2010
	Cross-strand disulfides in the hydrogen bonding site of antiparallel beta-sheet (aCSDhs): Forbidden disulfides that are highly strained, easily broken.	Haworth NL, Wouters MJ, Hunter MO, Ma L, Wouters MA.	Protein Sci	10.1002/pro.3545	2019
Phylogeny	Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park.	Kozubal MA, Romine M, Jennings Rd, Jay ZJ, Tringe SG, Rusch DB, Beam JP, McCue LA, Inskeep WP.	ISME J	10.1038/ismej.2012.132	2013
Metabolism	Down-state model of the voltage-sensing domain of a potassium channel.	Schow EV, Freites JA, Gogna K, White SH, Tobias DJ.	Biophys J	10.1016/j.bpj.2010.03.031	2010
Metabolism	Kinetic and thermodynamic features reveal that Escherichia coli BCP is an unusually versatile peroxiredoxin.	Reeves SA, Parsonage D, Nelson KJ, Poole LB.	Biochemistry	10.1021/bi200935d	2011
	Purine biosynthesis in archaea: variations on a theme.	Brown AM, Hoopes SL, White RH, Sarisky CA.	Biol Direct	10.1186/1745-6150-6-63	2011
Metabolism	New archaeal methyltransferases forming 1-methyladenosine or 1-methyladenosine and 1-methylguanosine at position 9 of tRNA.	Kempenaers M, Roovers M, Oudjama Y, Tkaczuk KL, Bujnicki JM, Droogmans L.	Nucleic Acids Res	10.1093/nar/gkq451	2010
Phylogeny	Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores.	Clarke GD, Beiko RG, Ragan MA, Charlebois RL.	J Bacteriol	10.1128/jb.184.8.2072-2080.2002	2002
Metabolism	Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon Pyrobaculum aerophilum.	Yang H, Fitz-Gibbon S, Marcotte EM, Tai JH, Hyman EC, Miller JH.	J Bacteriol	10.1128/jb.182.5.1272-1279.2000	2000
Metabolism	Crystal structure of Archaeoglobus fulgidus CTP:inositol-1-phosphate cytidylyltransferase, a key enzyme for di-myo-inositol-phosphate synthesis in (hyper)thermophiles.	Brito JA, Borges N, Vonrhein C, Santos H, Archer M.	J Bacteriol	10.1128/jb.01543-10	2011
	Characterization of an archaeal family 4 uracil DNA glycosylase and its interaction with PCNA and chromatin proteins.	Dionne I, Bell SD.	Biochem J	10.1042/bj20041661	2005
Metabolism	Structural basis of thermal stability of the tungsten cofactor synthesis protein MoaB from Pyrococcus furiosus.	Havarushka N, Fischer-Schrader K, Lamkemeyer T, Schwarz G.	PLoS One	10.1371/journal.pone.0086030	2014
	Agl24 is an ancient archaeal homolog of the eukaryotic N-glycan chitobiose synthesis enzymes.	Meyer BH, Adam PS, Wagstaff BA, Kolyfetis GE, Probst AJ, Albers SV, Dorfmueller HC.	Elife	10.7554/elife.67448	2022
Metabolism	Uracil recognition by replicative DNA polymerases is limited to the archaea, not occurring with bacteria and eukarya.	Wardle J, Burgers PM, Cann IK, Darley K, Heslop P, Johansson E, Lin LJ, McGlynn P, Sanvoisin J, Stith CM, Connolly BA.	Nucleic Acids Res	10.1093/nar/gkm1023	2008
	Biochemical and structural insights into RNA binding by Ssh10b, a member of the highly conserved Sac10b protein family in Archaea.	Guo L, Ding J, Guo R, Hou Y, Wang DC, Huang L.	J Biol Chem	10.1074/jbc.m113.521351	2014
Genetics	Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima.	Worning P, Jensen LJ, Nelson KE, Brunak S, Ussery DW.	Nucleic Acids Res	10.1093/nar/28.3.706	2000
Enzymology	The exopolyphosphatase gene from sulfolobus solfataricus: characterization of the first gene found to be involved in polyphosphate metabolism in archaea.	Cardona ST, Chavez FP, Jerez CA.	Appl Environ Microbiol	10.1128/aem.68.10.4812-4819.2002	2002
Metabolism	DNA end-directed and processive nuclease activities of the archaeal XPF enzyme.	Roberts JA, White MF.	Nucleic Acids Res	10.1093/nar/gki974	2005
Phylogeny	Annotation and Classification of CRISPR-Cas Systems.	Makarova KS, Koonin EV.	Methods Mol Biol	10.1007/978-1-4939-2687-9_4	2015
	Multiple replication origins with diverse control mechanisms in Haloarcula hispanica.	Wu Z, Liu J, Yang H, Liu H, Xiang H.	Nucleic Acids Res	10.1093/nar/gkt1214	2014
Metabolism	A Novel F420-dependent Thioredoxin Reductase Gated by Low Potential FAD: A TOOL FOR REDOX REGULATION IN AN ANAEROBE.	Susanti D, Loganathan U, Mukhopadhyay B.	J Biol Chem	10.1074/jbc.m116.750208	2016
	The major facilitator superfamily (MFS) revisited.	Reddy VS, Shlykov MA, Castillo R, Sun EI, Saier MH.	FEBS J	10.1111/j.1742-4658.2012.08588.x	2012
Metabolism	Structure of an acetyl-CoA binding protein from Staphylococcus aureus representing a novel subfamily of GCN5-related N-acetyltransferase-like proteins.	Cort JR, Ramelot TA, Murray D, Acton TB, Ma LC, Xiao R, Montelione GT, Kennedy MA.	J Struct Funct Genomics	10.1007/s10969-008-9041-z	2008
	The tRNA identity landscape for aminoacylation and beyond.	Giege R, Eriani G.	Nucleic Acids Res	10.1093/nar/gkad007	2023
Metabolism	The respiratory arsenite oxidase: structure and the role of residues surrounding the rieske cluster.	Warelow TP, Oke M, Schoepp-Cothenet B, Dahl JU, Bruselat N, Sivalingam GN, Leimkuhler S, Thalassinos K, Kappler U, Naismith JH, Santini JM.	PLoS One	10.1371/journal.pone.0072535	2013
	Systematizing the generation of missing metabolic knowledge.	Orth JD, Palsson BO.	Biotechnol Bioeng	10.1002/bit.22844	2010
	Participation of the S4 voltage sensor in the Mg2+-dependent activation of large conductance (BK) K+ channels.	Hu L, Shi J, Ma Z, Krishnamoorthy G, Sieling F, Zhang G, Horrigan FT, Cui J.	Proc Natl Acad Sci U S A	10.1073/pnas.1834300100	2003
	Multiple DNA binding domains mediate the function of the ERCC1-XPF protein in nucleotide excision repair.	Su Y, Orelli B, Madireddy A, Niedernhofer LJ, Scharer OD.	J Biol Chem	10.1074/jbc.m111.337899	2012
	Time-shared experiments for efficient assignment of triple-selectively labeled proteins.	Lohr F, Laguerre A, Bock C, Reckel S, Connolly PJ, Abdul-Manan N, Tumulka F, Abele R, Moore JM, Dotsch V.	J Magn Reson	10.1016/j.jmr.2014.09.014	2014
	Unique motifs identify PIG-A proteins from glycosyltransferases of the GT4 family.	Oswal N, Sahni NS, Bhattacharya A, Komath SS, Muthuswami R.	BMC Evol Biol	10.1186/1471-2148-8-168	2008
	Primordial soup or vinaigrette: did the RNA world evolve at acidic pH?	Bernhardt HS, Tate WP.	Biol Direct	10.1186/1745-6150-7-4	2012
Genetics	Identification of thermophilic species by the amino acid compositions deduced from their genomes.	Kreil DP, Ouzounis CA.	Nucleic Acids Res	10.1093/nar/29.7.1608	2001
	Cdc6-induced conformational changes in ORC bound to origin DNA revealed by cryo-electron microscopy.	Sun J, Kawakami H, Zech J, Speck C, Stillman B, Li H.	Structure	10.1016/j.str.2012.01.011	2012
Metabolism	Modelling insecticide-binding sites in the voltage-gated sodium channel.	O'Reilly AO, Khambay BP, Williamson MS, Field LM, Wallace BA, Davies TG.	Biochem J	10.1042/bj20051925	2006
Metabolism	eIF1A/eIF5B interaction network and its functions in translation initiation complex assembly and remodeling.	Nag N, Lin KY, Edmonds KA, Yu J, Nadkarni D, Marintcheva B, Marintchev A.	Nucleic Acids Res	10.1093/nar/gkw552	2016
Genetics	Re-annotation of genome microbial coding-sequences: finding new genes and inaccurately annotated genes.	Bocs S, Danchin A, Medigue C.	BMC Bioinformatics	10.1186/1471-2105-3-5	2002
Metabolism	Natural history of the E1-like superfamily: implication for adenylation, sulfur transfer, and ubiquitin conjugation.	Burroughs AM, Iyer LM, Aravind L.	Proteins	10.1002/prot.22298	2009
	Architecture and DNA recognition elements of the Fanconi anemia FANCM-FAAP24 complex.	Coulthard R, Deans AJ, Swuec P, Bowles M, Costa A, West SC, McDonald NQ.	Structure	10.1016/j.str.2013.07.006	2013
Metabolism	An uncharacterized member of the ribokinase family in Thermococcus kodakarensis exhibits myo-inositol kinase activity.	Sato T, Fujihashi M, Miyamoto Y, Kuwata K, Kusaka E, Fujita H, Miki K, Atomi H.	J Biol Chem	10.1074/jbc.m113.457259	2013
Metabolism	Characterization of the CRISPR/Cas subtype I-A system of the hyperthermophilic crenarchaeon Thermoproteus tenax.	Plagens A, Tjaden B, Hagemann A, Randau L, Hensel R.	J Bacteriol	10.1128/jb.00206-12	2012
Pathogenicity	Rifamycin antibiotic resistance by ADP-ribosylation: Structure and diversity of Arr.	Baysarowich J, Koteva K, Hughes DW, Ejim L, Griffiths E, Zhang K, Junop M, Wright GD.	Proc Natl Acad Sci U S A	10.1073/pnas.0711939105	2008
	Distinctive structural motifs co-ordinate the catalytic nucleophile and the residues of the oxyanion hole in the alpha/beta-hydrolase fold enzymes.	Dimitriou PS, Denesyuk AI, Nakayama T, Johnson MS, Denessiouk K.	Protein Sci	10.1002/pro.3527	2019
Metabolism	Plant, animal, and fungal micronutrient queuosine is salvaged by members of the DUF2419 protein family.	Zallot R, Brochier-Armanet C, Gaston KW, Forouhar F, Limbach PA, Hunt JF, de Crecy-Lagard V.	ACS Chem Biol	10.1021/cb500278k	2014
Enzymology	A self-compartmentalizing hexamer serine protease from Pyrococcus horikoshii: substrate selection achieved through multimerization.	Menyhard DK, Kiss-Szeman A, Tichy-Racs E, Hornung B, Radi K, Szeltner Z, Domokos K, Szamosi I, Naray-Szabo G, Polgar L, Harmat V.	J Biol Chem	10.1074/jbc.m113.451534	2013
	Pyrosequencing reveals high-temperature cellulolytic microbial consortia in Great Boiling Spring after in situ lignocellulose enrichment.	Peacock JP, Cole JK, Murugapiran SK, Dodsworth JA, Fisher JC, Moser DP, Hedlund BP.	PLoS One	10.1371/journal.pone.0059927	2013
	N-gram analysis of 970 microbial organisms reveals presence of biological language models.	Osmanbeyoglu HU, Ganapathiraju MK.	BMC Bioinformatics	10.1186/1471-2105-12-12	2011
	Land-use influences the distribution and activity of high affinity CO-oxidizing bacteria associated to type I-coxL genotype in soil.	Quiza L, Lalonde I, Guertin C, Constant P.	Front Microbiol	10.3389/fmicb.2014.00271	2014
	Nitrite-reductase and peroxynitrite isomerization activities of Methanosarcina acetivorans protoglobin.	Ascenzi P, Leboffe L, Pesce A, Ciaccio C, Sbardella D, Bolognesi M, Coletta M.	PLoS One	10.1371/journal.pone.0095391	2014
	Enigmatic, ultrasmall, uncultivated Archaea.	Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, Verberkmoes NC, Hettich RL, Banfield JF.	Proc Natl Acad Sci U S A	10.1073/pnas.0914470107	2010
Pathogenicity	Molecular determinants of KCNQ (Kv7) K+ channel sensitivity to the anticonvulsant retigabine.	Schenzer A, Friedrich T, Pusch M, Saftig P, Jentsch TJ, Grotzinger J, Schwake M.	J Neurosci	10.1523/jneurosci.0128-05.2005	2005
Genetics	A conserved MCM single-stranded DNA binding element is essential for replication initiation.	Froelich CA, Kang S, Epling LB, Bell SP, Enemark EJ.	Elife	10.7554/elife.01993	2014
	Structural characterization of the voltage-sensor domain and voltage-gated K+-channel proteins vectorially oriented within a single bilayer membrane at the solid/vapor and solid/liquid interfaces via neutron interferometry.	Gupta S, Dura JA, Freites JA, Tobias DJ, Blasie JK.	Langmuir	10.1021/la301219z	2012
	Evaluating the efficacy of tryptophan fluorescence and absorbance as a selection tool for identifying protein crystals.	Gill HS.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309110002022	2010
Metabolism	Entropic stabilization of proteins and its proteomic consequences.	Berezovsky IN, Chen WW, Choi PJ, Shakhnovich EI.	PLoS Comput Biol	10.1371/journal.pcbi.0010047	2005
Metabolism	Characterization of an archaeal two-component system that regulates methanogenesis in Methanosaeta harundinacea.	Li J, Zheng X, Guo X, Qi L, Dong X.	PLoS One	10.1371/journal.pone.0095502	2014
Enzymology	Cloning and characterization of a family B DNA polymerase from the hyperthermophilic crenarchaeon Pyrobaculum islandicum.	Kahler M, Antranikian G.	J Bacteriol	10.1128/jb.182.3.655-663.2000	2000
Metabolism	Activity and transcriptional regulation of bacterial protein-like glycerol-3-phosphate dehydrogenase of the haloarchaea in Haloferax volcanii.	Rawls KS, Martin JH, Maupin-Furlow JA.	J Bacteriol	10.1128/jb.00276-11	2011
Metabolism	The elusive third subunit IIa of the bacterial B-type oxidases: the enzyme from the hyperthermophile Aquifex aeolicus.	Prunetti L, Brugna M, Lebrun R, Giudici-Orticoni MT, Guiral M.	PLoS One	10.1371/journal.pone.0021616	2011
	Low rates of lateral gene transfer among metabolic genes define the evolving biogeochemical niches of archaea through deep time.	Blank CE.	Archaea	10.1155/2012/843539	2012
Genetics	Lineage-specific gene expansions in bacterial and archaeal genomes.	Jordan IK, Makarova KS, Spouge JL, Wolf YI, Koonin EV.	Genome Res	10.1101/gr.gr-1660r	2001
	Voltage-dependent conformational changes of KVAP S4 segment in bacterial membrane environment.	Koag MC, Papazian DM.	Channels (Austin)	10.4161/chan.3.5.9697	2009
Metabolism	Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis.	Plapp BV, Savarimuthu BR, Ferraro DJ, Rubach JK, Brown EN, Ramaswamy S.	Biochemistry	10.1021/acs.biochem.7b00446	2017
	The complete genome sequence and emendation of the hyperthermophilic, obligate iron-reducing archaeon "Geoglobus ahangari" strain 234(T).	Manzella MP, Holmes DE, Rocheleau JM, Chung A, Reguera G, Kashefi K.	Stand Genomic Sci	10.1186/s40793-015-0035-8	2015
	High-resolution orientation and depth of insertion of the voltage-sensing S4 helix of a potassium channel in lipid bilayers.	Doherty T, Su Y, Hong M.	J Mol Biol	10.1016/j.jmb.2010.06.048	2010
Enzymology	Modelling the evolution of the archeal tryptophan synthase.	Merkl R.	BMC Evol Biol	10.1186/1471-2148-7-59	2007
	An analysis of amino acid sequences surrounding archaeal glycoprotein sequons.	Abu-Qarn M, Eichler J.	Archaea	10.1155/2006/510578	2007
Metabolism	A unique insert of leucyl-tRNA synthetase is required for aminoacylation and not amino acid editing.	Vu MT, Martinis SA.	Biochemistry	10.1021/bi062078j	2007
Metabolism	GO4genome: a prokaryotic phylogeny based on genome organization.	Merkl R, Wiezer A.	J Mol Evol	10.1007/s00239-009-9233-6	2009
Enzymology	Biochemical properties and base excision repair complex formation of apurinic/apyrimidinic endonuclease from Pyrococcus furiosus.	Kiyonari S, Tahara S, Shirai T, Iwai S, Ishino S, Ishino Y.	Nucleic Acids Res	10.1093/nar/gkp720	2009
Enzymology	The complex structures of isocitrate dehydrogenase from Clostridium thermocellum and Desulfotalea psychrophila suggest a new active site locking mechanism.	Leiros HK, Fedoy AE, Leiros I, Steen IH.	FEBS Open Bio	10.1016/j.fob.2012.06.003	2012
	SIGI: score-based identification of genomic islands.	Merkl R.	BMC Bioinformatics	10.1186/1471-2105-5-22	2004
Metabolism	Structural basis for catalysis at the membrane-water interface.	Dufrisne MB, Petrou VI, Clarke OB, Mancia F.	Biochim Biophys Acta Mol Cell Biol Lipids	10.1016/j.bbalip.2016.11.011	2017
Metabolism	Molecular determinants of origin discrimination by Orc1 initiators in archaea.	Dueber EC, Costa A, Corn JE, Bell SD, Berger JM.	Nucleic Acids Res	10.1093/nar/gkq1308	2011
Metabolism	A domain for editing by an archaebacterial tRNA synthetase.	Beebe K, Merriman E, Ribas De Pouplana L, Schimmel P.	Proc Natl Acad Sci U S A	10.1073/pnas.0401530101	2004
Metabolism	Reconstruction of the archaeal isoprenoid ether lipid biosynthesis pathway in Escherichia coli through digeranylgeranylglyceryl phosphate.	Lai D, Lluncor B, Schroder I, Gunsalus RP, Liao JC, Monbouquette HG.	Metab Eng	10.1016/j.ymben.2009.01.008	2009
Genetics	Analysis of the crystal structure of an active MCM hexamer.	Miller JM, Arachea BT, Epling LB, Enemark EJ.	Elife	10.7554/elife.03433	2014
Genetics	Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea.	Yelton AP, Comolli LR, Justice NB, Castelle C, Denef VJ, Thomas BC, Banfield JF.	BMC Genomics	10.1186/1471-2164-14-485	2013
Metabolism	Complete genome sequence of the anaerobic, protein-degrading hyperthermophilic crenarchaeon Desulfurococcus kamchatkensis.	Ravin NV, Mardanov AV, Beletsky AV, Kublanov IV, Kolganova TV, Lebedinsky AV, Chernyh NA, Bonch-Osmolovskaya EA, Skryabin KG.	J Bacteriol	10.1128/jb.01525-08	2009
Metabolism	Uncovering the human methyltransferasome.	Petrossian TC, Clarke SG.	Mol Cell Proteomics	10.1074/mcp.m110.000976	2011
	Revisiting the structure/function relationships of H/ACA(-like) RNAs: a unified model for Euryarchaea and Crenarchaea.	Toffano-Nioche C, Gautheret D, Leclerc F.	Nucleic Acids Res	10.1093/nar/gkv756	2015
Genetics	Genome-wide survey of prokaryotic serine proteases: analysis of distribution and domain architectures of five serine protease families in prokaryotes.	Tripathi LP, Sowdhamini R.	BMC Genomics	10.1186/1471-2164-9-549	2008
Phylogeny	A phylogenomic profile of globins.	Vinogradov SN, Hoogewijs D, Bailly X, Arredondo-Peter R, Gough J, Dewilde S, Moens L, Vanfleteren JR.	BMC Evol Biol	10.1186/1471-2148-6-31	2006
Phylogeny	Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces.	Beja O, Koonin EV, Aravind L, Taylor LT, Seitz H, Stein JL, Bensen DC, Feldman RA, Swanson RV, DeLong EF.	Appl Environ Microbiol	10.1128/aem.68.1.335-345.2002	2002
	Structural basis for the recruitment of ERCC1-XPF to nucleotide excision repair complexes by XPA.	Tsodikov OV, Ivanov D, Orelli B, Staresincic L, Shoshani I, Oberman R, Scharer OD, Wagner G, Ellenberger T.	EMBO J	10.1038/sj.emboj.7601894	2007
Metabolism	A novel biosynthetic pathway of archaetidyl-myo-inositol via archaetidyl-myo-inositol phosphate from CDP-archaeol and D-glucose 6-phosphate in methanoarchaeon Methanothermobacter thermautotrophicus cells.	Morii H, Kiyonari S, Ishino Y, Koga Y.	J Biol Chem	10.1074/jbc.m109.034652	2009
	A genetic approach for analyzing the co-operative function of the tRNA mimicry complex, eRF1/eRF3, in translation termination on the ribosome.	Wada M, Ito K.	Nucleic Acids Res	10.1093/nar/gku493	2014
Metabolism	Presence of a classical RRM-fold palm domain in Thg1-type 3'- 5'nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains.	Anantharaman V, Iyer LM, Aravind L.	Biol Direct	10.1186/1745-6150-5-43	2010
Genetics	Applying negative rule mining to improve genome annotation.	Artamonova II, Frishman G, Frishman D.	BMC Bioinformatics	10.1186/1471-2105-8-261	2007
Metabolism	Displacement of the canonical single-stranded DNA-binding protein in the Thermoproteales.	Paytubi S, McMahon SA, Graham S, Liu H, Botting CH, Makarova KS, Koonin EV, Naismith JH, White MF.	Proc Natl Acad Sci U S A	10.1073/pnas.1113277108	2012
Metabolism	New insights on the mechanism of the K(+-) independent activity of crenarchaeota pyruvate kinases.	De la Vega-Ruiz G, Dominguez-Ramirez L, Riveros-Rosas H, Guerrero-Mendiola C, Torres-Larios A, Hernandez-Alcantara G, Garcia-Trejo JJ, Ramirez-Silva L.	PLoS One	10.1371/journal.pone.0119233	2015
	Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins.	Makarova KS, Ponomarev VA, Koonin EV.	Genome Biol	10.1186/gb-2001-2-9-research0033	2001
Metabolism	Molecular template for a voltage sensor in a novel K+ channel. III. Functional reconstitution of a sensorless pore module from a prokaryotic Kv channel.	Santos JS, Grigoriev SM, Montal M.	J Gen Physiol	10.1085/jgp.200810077	2008
	Combinatorial triple-selective labeling as a tool to assist membrane protein backbone resonance assignment.	Lohr F, Reckel S, Karbyshev M, Connolly PJ, Abdul-Manan N, Bernhard F, Moore JM, Dotsch V.	J Biomol NMR	10.1007/s10858-012-9601-1	2012
Genetics	Fine-structured multi-scaling long-range correlations in completely sequenced genomes--features, origin, and classification.	Knoch TA, Goker M, Lohner R, Abuseiris A, Grosveld FG.	Eur Biophys J	10.1007/s00249-009-0489-y	2009
Metabolism	Functional characterization of the vitamin K2 biosynthetic enzyme UBIAD1.	Hirota Y, Nakagawa K, Sawada N, Okuda N, Suhara Y, Uchino Y, Kimoto T, Funahashi N, Kamao M, Tsugawa N, Okano T.	PLoS One	10.1371/journal.pone.0125737	2015
Metabolism	Aminoacyl-tRNA-charged eukaryotic elongation factor 1A is the bona fide substrate for Legionella pneumophila effector glucosyltransferases.	Tzivelekidis T, Jank T, Pohl C, Schlosser A, Rospert S, Knudsen CR, Rodnina MV, Belyi Y, Aktories K.	PLoS One	10.1371/journal.pone.0029525	2011
Genetics	Lineage-specific partitions in archaeal transcription.	Coulson RM, Touboul N, Ouzounis CA.	Archaea	10.1155/2006/629868	2007
Metabolism	A highly selective oligopeptide binding protein from the archaeon Sulfolobus solfataricus.	Gogliettino M, Balestrieri M, Pocsfalvi G, Fiume I, Natale L, Rossi M, Palmieri G.	J Bacteriol	10.1128/jb.01414-09	2010
Genetics	GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.	Besemer J, Lomsadze A, Borodovsky M.	Nucleic Acids Res	10.1093/nar/29.12.2607	2001
Metabolism	Characterization of a heme-dependent catalase from Methanobrevibacter arboriphilus.	Shima S, Sordel-Klippert M, Brioukhanov A, Netrusov A, Linder D, Thauer RK.	Appl Environ Microbiol	10.1128/aem.67.7.3041-3045.2001	2001
Metabolism	Genomewide and biochemical analyses of DNA-binding activity of Cdc6/Orc1 and Mcm proteins in Pyrococcus sp.	Matsunaga F, Glatigny A, Mucchielli-Giorgi MH, Agier N, Delacroix H, Marisa L, Durosay P, Ishino Y, Aggerbeck L, Forterre P.	Nucleic Acids Res	10.1093/nar/gkm212	2007
	Cross-reactivity of peanut allergens.	Bublin M, Breiteneder H.	Curr Allergy Asthma Rep	10.1007/s11882-014-0426-8	2014
Metabolism	A gating model for the archeal voltage-dependent K(+) channel KvAP in DPhPC and POPE:POPG decane lipid bilayers.	Schmidt D, Cross SR, MacKinnon R.	J Mol Biol	10.1016/j.jmb.2009.05.062	2009
Metabolism	The heteromeric Nanoarchaeum equitans splicing endonuclease cleaves noncanonical bulge-helix-bulge motifs of joined tRNA halves.	Randau L, Calvin K, Hall M, Yuan J, Podar M, Li H, Soll D.	Proc Natl Acad Sci U S A	10.1073/pnas.0509197102	2005
	Translation in giant viruses: a unique mixture of bacterial and eukaryotic termination schemes.	Jeudy S, Abergel C, Claverie JM, Legendre M.	PLoS Genet	10.1371/journal.pgen.1003122	2012
	Many nonuniversal archaeal ribosomal proteins are found in conserved gene clusters.	Wang J, Dasgupta I, Fox GE.	Archaea	10.1155/2009/971494	2009
Phylogeny	Comparing the Dictyostelium and Entamoeba genomes reveals an ancient split in the Conosa lineage.	Song J, Xu Q, Olsen R, Loomis WF, Shaulsky G, Kuspa A, Sucgang R.	PLoS Comput Biol	10.1371/journal.pcbi.0010071	2005
	Membrane protein prediction methods.	Punta M, Forrest LR, Bigelow H, Kernytsky A, Liu J, Rost B.	Methods	10.1016/j.ymeth.2006.07.026	2007
Metabolism	Formation of m2G6 in Methanocaldococcus jannaschii tRNA catalyzed by the novel methyltransferase Trm14.	Menezes S, Gaston KW, Krivos KL, Apolinario EE, Reich NO, Sowers KR, Limbach PA, Perona JJ.	Nucleic Acids Res	10.1093/nar/gkr475	2011
Metabolism	PCNA and XPF cooperate to distort DNA substrates.	Hutton RD, Craggs TD, White MF, Penedo JC.	Nucleic Acids Res	10.1093/nar/gkp1104	2010
	Archaeal signal peptides--a comparative survey at the genome level.	Bardy SL, Eichler J, Jarrell KF.	Protein Sci	10.1110/ps.03148703	2003
	Revisiting the operational RNA code for amino acids: Ensemble attributes and their implications.	Shaul S, Berel D, Benjamini Y, Graur D.	RNA	10.1261/rna.1745910	2010
Metabolism	A transposon-derived DNA polymerase from Entamoeba histolytica displays intrinsic strand displacement, processivity and lesion bypass.	Pastor-Palacios G, Lopez-Ramirez V, Cardona-Felix CS, Brieba LG.	PLoS One	10.1371/journal.pone.0049964	2012
	Molecular modeling of the bifunctional enzyme UDP-GlcNAc 2-epimerase/ManNAc kinase and predictions of structural effects of mutations associated with HIBM and sialuria.	Kurochkina N, Yardeni T, Huizing M.	Glycobiology	10.1093/glycob/cwp176	2010
Phylogeny	The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods.	McCann A, Cotton JA, McInerney JO.	BMC Evol Biol	10.1186/1471-2148-8-312	2008
Phylogeny	In silico detection of tRNA sequence features characteristic to aminoacyl-tRNA synthetase class membership.	Jako E, Ittzes P, Szenes A, Kun A, Szathmary E, Pal G.	Nucleic Acids Res	10.1093/nar/gkm598	2007
Enzymology	Characterization of a zinc-containing alcohol dehydrogenase with stereoselectivity from the hyperthermophilic archaeon Thermococcus guaymasensis.	Ying X, Ma K.	J Bacteriol	10.1128/jb.01433-10	2011
	Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures.	Pride DT, Schoenfeld T.	BMC Genomics	10.1186/1471-2164-9-420	2008
Metabolism	Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis.	Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR.	PLoS One	10.1371/journal.pone.0016626	2011
Enzymology	Identification of an alternative nucleoside triphosphate: 5'-deoxyadenosylcobinamide phosphate nucleotidyltransferase in Methanobacterium thermoautotrophicum delta H.	Thomas MG, Escalante-Semerena JC.	J Bacteriol	10.1128/jb.182.15.4227-4233.2000	2000
Metabolism	Bacillus subtilis GlcK activity requires cysteines within a motif that discriminates microbial glucokinases into two lineages.	Mesak LR, Mesak FM, Dahl MK.	BMC Microbiol	10.1186/1471-2180-4-6	2004
Metabolism	Molecular analyses of a three-subunit euryarchaeal clamp loader complex from Methanosarcina acetivorans.	Chen YH, Lin Y, Yoshinaga A, Chhotani B, Lorenzini JL, Crofts AA, Mei S, Mackie RI, Ishino Y, Cann IK.	J Bacteriol	10.1128/jb.00414-09	2009
	Analysis of the XPA and ssDNA-binding surfaces on the central domain of human ERCC1 reveals evidence for subfunctionalization.	Tripsianes K, Folkers GE, Zheng C, Das D, Grinstead JS, Kaptein R, Boelens R.	Nucleic Acids Res	10.1093/nar/gkm503	2007
Metabolism	The human Kv1.1 channel is palmitoylated, modulating voltage sensing: Identification of a palmitoylation consensus sequence.	Gubitosi-Klug RA, Mancuso DJ, Gross RW.	Proc Natl Acad Sci U S A	10.1073/pnas.0501999102	2005
	ProtRepeatsDB: a database of amino acid repeats in genomes.	Kalita MK, Ramasamy G, Duraisamy S, Chauhan VS, Gupta D.	BMC Bioinformatics	10.1186/1471-2105-7-336	2006
	Molecular architecture and divalent cation activation of TvoK, a prokaryotic potassium channel.	Parfenova LV, Abarca-Heidemann K, Crane BM, Rothberg BS.	J Biol Chem	10.1074/jbc.m703650200	2007
	bSUM: A bead-supported unilamellar membrane system facilitating unidirectional insertion of membrane proteins into giant vesicles.	Zheng H, Lee S, Llaguno MC, Jiang QX.	J Gen Physiol	10.1085/jgp.201511448	2016
Enzymology	Paths of lateral gene transfer of lysyl-aminoacyl-tRNA synthetases with a unique evolutionary transition stage of prokaryotes coding for class I and II varieties by the same organisms.	Shaul S, Nussinov R, Pupko T.	BMC Evol Biol	10.1186/1471-2148-6-22	2006
	Large-scale comparative genomic ranking of taxonomically restricted genes (TRGs) in bacterial and archaeal genomes.	Wilson GA, Feil EJ, Lilley AK, Field D.	PLoS One	10.1371/journal.pone.0000324	2007
	Evolution of gene fusions: horizontal transfer versus independent events.	Yanai I, Wolf YI, Koonin EV.	Genome Biol	10.1186/gb-2002-3-5-research0024	2002
Metabolism	An archaeal Rad54 protein remodels DNA and stimulates DNA strand exchange by RadA.	Haseltine CA, Kowalczykowski SC.	Nucleic Acids Res	10.1093/nar/gkp068	2009
	Statistical evaluation of the Rodin-Ohno hypothesis: sense/antisense coding of ancestral class I and II aminoacyl-tRNA synthetases.	Chandrasekaran SN, Yardimci GG, Erdogan O, Roach J, Carter CW.	Mol Biol Evol	10.1093/molbev/mst070	2013
Metabolism	Identification and characterization of oxalate oxidoreductase, a novel thiamine pyrophosphate-dependent 2-oxoacid oxidoreductase that enables anaerobic growth on oxalate.	Pierce E, Becker DF, Ragsdale SW.	J Biol Chem	10.1074/jbc.m110.155739	2010
	A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans.	Podar M, Anderson I, Makarova KS, Elkins JG, Ivanova N, Wall MA, Lykidis A, Mavromatis K, Sun H, Hudson ME, Chen W, Deciu C, Hutchison D, Eads JR, Anderson A, Fernandes F, Szeto E, Lapidus A, Kyrpides NC, Saier MH, Richardson PM, Rachel R, Huber H, Eisen JA, Koonin EV, Keller M, Stetter KO.	Genome Biol	10.1186/gb-2008-9-11-r158	2008
Enzymology	The emerging periplasm-localized subclass of AroQ chorismate mutases, exemplified by those from Salmonella typhimurium and Pseudomonas aeruginosa.	Calhoun DH, Bonner CA, Gu W, Xie G, Jensen RA.	Genome Biol	10.1186/gb-2001-2-8-research0030	2001
Metabolism	Gating of the bacterial sodium channel, NaChBac: voltage-dependent charge movement and gating currents.	Kuzmenkin A, Bezanilla F, Correa AM.	J Gen Physiol	10.1085/jgp.200409139	2004
Enzymology	Arsenite oxidase aox genes from a metal-resistant beta-proteobacterium.	Muller D, Lievremont D, Simeonova DD, Hubert JC, Lett MC.	J Bacteriol	10.1128/jb.185.1.135-141.2003	2003
Genetics	Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction.	Anderson I, Rodriguez J, Susanti D, Porat I, Reich C, Ulrich LE, Elkins JG, Mavromatis K, Lykidis A, Kim E, Thompson LS, Nolan M, Land M, Copeland A, Lapidus A, Lucas S, Detter C, Zhulin IB, Olsen GJ, Whitman W, Mukhopadhyay B, Bristow J, Kyrpides N.	J Bacteriol	10.1128/jb.01949-07	2008
	The catalytic domains of thiamine triphosphatase and CyaB-like adenylyl cyclase define a novel superfamily of domains that bind organic phosphates.	Iyer LM, Aravind L.	BMC Genomics	10.1186/1471-2164-3-33	2002
	The K-loop, a general feature of the Pyrococcus C/D guide RNAs, is an RNA structural motif related to the K-turn.	Nolivos S, Carpousis AJ, Clouet-d'Orval B.	Nucleic Acids Res	10.1093/nar/gki962	2005
Metabolism	Predicted class-I aminoacyl tRNA synthetase-like proteins in non-ribosomal peptide synthesis.	Aravind L, de Souza RF, Iyer LM.	Biol Direct	10.1186/1745-6150-5-48	2010
Metabolism	The Potato Nucleotide-binding Leucine-rich Repeat (NLR) Immune Receptor Rx1 Is a Pathogen-dependent DNA-deforming Protein.	Fenyk S, Townsend PD, Dixon CH, Spies GB, de San Eustaquio Campillo A, Slootweg EJ, Westerhof LB, Gawehns FK, Knight MR, Sharples GJ, Goverse A, Palsson LO, Takken FL, Cann MJ.	J Biol Chem	10.1074/jbc.m115.672121	2015
Metabolism	Biosynthesis of ubiquinone compounds with conjugated prenyl side chains.	Lee PC, Salomon C, Mijts B, Schmidt-Dannert C.	Appl Environ Microbiol	10.1128/aem.01495-08	2008
Metabolism	Acylpeptide hydrolase inhibition as targeted strategy to induce proteasomal down-regulation.	Palmieri G, Bergamo P, Luini A, Ruvo M, Gogliettino M, Langella E, Saviano M, Hegde RN, Sandomenico A, Rossi M.	PLoS One	10.1371/journal.pone.0025888	2011
Metabolism	Characterization of two methanopterin biosynthesis mutants of Methylobacterium extorquens AM1 by use of a tetrahydromethanopterin bioassay.	Rasche ME, Havemann SA, Rosenzvaig M.	J Bacteriol	10.1128/jb.186.5.1565-1570.2004	2004
Phylogeny	Visualization of the phylogenetic content of five genomes using dekapentagonal maps.	Zhaxybayeva O, Hamel L, Raymond J, Gogarten JP.	Genome Biol	10.1186/gb-2004-5-3-r20	2004
	Bacterial regulatory networks are extremely flexible in evolution.	Lozada-Chavez I, Janga SC, Collado-Vides J.	Nucleic Acids Res	10.1093/nar/gkl423	2006
Metabolism	Generation, comparison, and merging of pathways between protein conformations: gating in K-channels.	Enosh A, Raveh B, Furman-Schueler O, Halperin D, Ben-Tal N.	Biophys J	10.1529/biophysj.108.135285	2008
	Domain architecture conservation in orthologs.	Forslund K, Pekkari I, Sonnhammer EL.	BMC Bioinformatics	10.1186/1471-2105-12-326	2011
Enzymology	The structure of an archaeal homodimeric ligase which has RNA circularization activity.	Brooks MA, Meslet-Cladiere L, Graille M, Kuhn J, Blondeau K, Myllykallio H, van Tilbeurgh H.	Protein Sci	10.1110/ps.035493.108	2008
Genetics	An improved probability mapping approach to assess genome mosaicism.	Zhaxybayeva O, Gogarten JP.	BMC Genomics	10.1186/1471-2164-4-37	2003
Metabolism	Hjm/Hel308A DNA helicase from Sulfolobus tokodaii promotes replication fork regression and interacts with Hjc endonuclease in vitro.	Li Z, Lu S, Hou G, Ma X, Sheng D, Ni J, Shen Y.	J Bacteriol	10.1128/jb.01662-07	2008
	Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses.	Zhaxybayeva O, Gogarten JP.	BMC Genomics	10.1186/1471-2164-3-4	2002
	The molecular evolution of the Qo motif.	Kao WC, Hunte C.	Genome Biol Evol	10.1093/gbe/evu147	2014
Metabolism	An integrated understanding of the physiological response to elevated extracellular phosphate.	Camalier CE, Yi M, Yu LR, Hood BL, Conrads KA, Lee YJ, Lin Y, Garneys LM, Bouloux GF, Young MR, Veenstra TD, Stephens RM, Colburn NH, Conrads TP, Beck GR.	J Cell Physiol	10.1002/jcp.24312	2013
	Structure of the Cdt1 C-terminal domain: conservation of the winged helix fold in replication licensing factors.	Khayrutdinov BI, Bae WJ, Yun YM, Lee JH, Tsuyama T, Kim JJ, Hwang E, Ryu KS, Cheong HK, Cheong C, Ko JS, Enomoto T, Karplus PA, Guntert P, Tada S, Jeon YH, Cho Y.	Protein Sci	10.1002/pro.236	2009
Enzymology	A study of archaeal enzymes involved in polar lipid synthesis linking amino acid sequence information, genomic contexts and lipid composition.	Daiyasu H, Kuma K, Yokoi T, Morii H, Koga Y, Toh H.	Archaea	10.1155/2005/452563	2005
Enzymology	Nonmarine crenarchaeol in Nevada hot springs.	Pearson A, Huang Z, Ingalls AE, Romanek CS, Wiegel J, Freeman KH, Smittenberg RH, Zhang CL.	Appl Environ Microbiol	10.1128/aem.70.9.5229-5237.2004	2004
Metabolism	Identification and characterization of phosphoseryl-tRNA[Ser]Sec kinase.	Carlson BA, Xu XM, Kryukov GV, Rao M, Berry MJ, Gladyshev VN, Hatfield DL.	Proc Natl Acad Sci U S A	10.1073/pnas.0402636101	2004
Metabolism	A freestanding proofreading domain is required for protein synthesis quality control in Archaea.	Korencic D, Ahel I, Schelert J, Sacher M, Ruan B, Stathopoulos C, Blum P, Ibba M, Soll D.	Proc Natl Acad Sci U S A	10.1073/pnas.0403926101	2004
	Structure and haem-distal site plasticity in Methanosarcina acetivorans protoglobin.	Pesce A, Tilleman L, Donne J, Aste E, Ascenzi P, Ciaccio C, Coletta M, Moens L, Viappiani C, Dewilde S, Bolognesi M, Nardini M.	PLoS One	10.1371/journal.pone.0066144	2013
Metabolism	A biochemically active MCM-like helicase in Bacillus cereus.	Samuels M, Gulati G, Shin JH, Opara R, McSweeney E, Sekedat M, Long S, Kelman Z, Jeruzalmi D.	Nucleic Acids Res	10.1093/nar/gkp376	2009
Metabolism	3-hydroxypropionyl-coenzyme A dehydratase and acryloyl-coenzyme A reductase, enzymes of the autotrophic 3-hydroxypropionate/4-hydroxybutyrate cycle in the Sulfolobales.	Teufel R, Kung JW, Kockelkorn D, Alber BE, Fuchs G.	J Bacteriol	10.1128/jb.00068-09	2009
	Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications.	Marck C, Grosjean H.	RNA	10.1261/rna.5132503	2003
	Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms.	Tsunoda M, Kusakabe Y, Tanaka N, Ohno S, Nakamura M, Senda T, Moriguchi T, Asai N, Sekine M, Yokogawa T, Nishikawa K, Nakamura KT.	Nucleic Acids Res	10.1093/nar/gkm417	2007
Enzymology	Identification of an Archaeal type II isopentenyl diphosphate isomerase in methanothermobacter thermautotrophicus.	Barkley SJ, Cornish RM, Poulter CD.	J Bacteriol	10.1128/jb.186.6.1811-1817.2004	2004
Metabolism	Functional influence of the pore helix glutamate in the KcsA K+ channel.	Choi H, Heginbotham L.	Biophys J	10.1016/s0006-3495(04)74273-3	2004
Metabolism	The cbiS gene of the archaeon Methanopyrus kandleri AV19 encodes a bifunctional enzyme with adenosylcobinamide amidohydrolase and alpha-ribazole-phosphate phosphatase activities.	Woodson JD, Escalante-Semerena JC.	J Bacteriol	10.1128/jb.00227-06	2006
Stress	A comprehensive census of microbial diversity in hot springs of Tengchong, Yunnan Province China using 16S rRNA gene pyrosequencing.	Hou W, Wang S, Dong H, Jiang H, Briggs BR, Peacock JP, Huang Q, Huang L, Wu G, Zhi X, Li W, Dodsworth JA, Hedlund BP, Zhang C, Hartnett HE, Dijkstra P, Hungate BA.	PLoS One	10.1371/journal.pone.0053350	2013
Metabolism	An archaebacteria-derived glutamyl-tRNA synthetase and tRNA pair for unnatural amino acid mutagenesis of proteins in Escherichia coli.	Santoro SW, Anderson JC, Lakshman V, Schultz PG.	Nucleic Acids Res	10.1093/nar/gkg903	2003
Enzymology	Mercury adaptation among bacteria from a deep-sea hydrothermal vent.	Vetriani C, Chew YS, Miller SM, Yagi J, Coombs J, Lutz RA, Barkay T.	Appl Environ Microbiol	10.1128/aem.71.1.220-226.2005	2005
Phylogeny	BranchClust: a phylogenetic algorithm for selecting gene families.	Poptsova MS, Gogarten JP.	BMC Bioinformatics	10.1186/1471-2105-8-120	2007
Metabolism	Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification.	Haft DH, Payne SH, Selengut JD.	J Bacteriol	10.1128/jb.06026-11	2012
Metabolism	Contribution of hydrophobic and electrostatic interactions to the membrane integration of the Shaker K+ channel voltage sensor domain.	Zhang L, Sato Y, Hessa T, von Heijne G, Lee JK, Kodama I, Sakaguchi M, Uozumi N.	Proc Natl Acad Sci U S A	10.1073/pnas.0611007104	2007
	Biological diversity in the patent system.	Oldham P, Hall S, Forero O.	PLoS One	10.1371/journal.pone.0078737	2013
	Evidence for symmetric chromosomal inversions around the replication origin in bacteria.	Eisen JA, Heidelberg JF, White O, Salzberg SL.	Genome Biol	10.1186/gb-2000-1-6-research0011	2000
Metabolism	Proteolysis in hyperthermophilic microorganisms.	Ward DE, Shockley KR, Chang LS, Levy RD, Michel JK, Conners SB, Kelly RM.	Archaea	10.1155/2002/503191	2002
	DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches.	Thompson JD, Plewniak F, Thierry J, Poch O.	Nucleic Acids Res	10.1093/nar/28.15.2919	2000
Metabolism	Transfer RNA-dependent amino acid biosynthesis: an essential route to asparagine formation.	Min B, Pelaschier JT, Graham DE, Tumbula-Hansen D, Soll D.	Proc Natl Acad Sci U S A	10.1073/pnas.012027399	2002
Metabolism	An abundant DNA binding protein from the hyperthermophilic archaeon Sulfolobus shibatae affects DNA supercoiling in a temperature-dependent fashion.	Xue H, Guo R, Wen Y, Liu D, Huang L.	J Bacteriol	10.1128/jb.182.14.3929-3933.2000	2000
	Thermodynamics of voltage-gated ion channels.	Zhang XC, Yang H, Liu Z, Sun F.	Biophys Rep	10.1007/s41048-018-0074-y	2018
	Application of a Colorimetric Assay to Identify Putative Ribofuranosylaminobenzene 5'-Phosphate Synthase Genes Expressed with Activity in Escherichia coli.	Bechard ME, Chhatwal S, Garcia RE, Rasche ME.	Biol Proced Online	10.1251/bpo48	2003
Genetics	A genomic timescale for the origin of eukaryotes.	Hedges SB, Chen H, Kumar S, Wang DY, Thompson AS, Watanabe H.	BMC Evol Biol	10.1186/1471-2148-1-4	2001
	Adaptive role of increased frequency of polypurine tracts in mRNA sequences of thermophilic prokaryotes.	Paz A, Mester D, Baca I, Nevo E, Korol A.	Proc Natl Acad Sci U S A	10.1073/pnas.0308594100	2004
Metabolism	Characterization of a novel zinc-containing, lysine-specific aminopeptidase from the hyperthermophilic archaeon Pyrococcus furiosus.	Story SV, Shah C, Jenney FE, Adams MW, Adams MW.	J Bacteriol	10.1128/jb.187.6.2077-2083.2005	2005
Genetics	Systematic association of genes to phenotypes by genome and literature mining.	Korbel JO, Doerks T, Jensen LJ, Perez-Iratxeta C, Kaczanowski S, Hooper SD, Andrade MA, Bork P.	PLoS Biol	10.1371/journal.pbio.0030134	2005
Enzymology	Crystal structures from the Plasmodium peroxiredoxins: new insights into oligomerization and product binding.	Qiu W, Dong A, Pizarro JC, Botchkarsev A, Min J, Wernimont AK, Hills T, Hui R, Artz JD.	BMC Struct Biol	10.1186/1472-6807-12-2	2012
	Structure of Alba: an archaeal chromatin protein modulated by acetylation.	Wardleworth BN, Russell RJ, Bell SD, Taylor GL, White MF.	EMBO J	10.1093/emboj/cdf465	2002
Pathogenicity	The role of PerR in O2-affected gene expression of Clostridium acetobutylicum.	Hillmann F, Doring C, Riebe O, Ehrenreich A, Fischer RJ, Bahl H.	J Bacteriol	10.1128/jb.00351-09	2009
Metabolism	Identification and properties of the crenarchaeal single-stranded DNA binding protein from Sulfolobus solfataricus.	Wadsworth RI, White MF.	Nucleic Acids Res	10.1093/nar/29.4.914	2001
Phylogeny	Genome trees from conservation profiles.	Tekaia F, Yeramian E.	PLoS Comput Biol	10.1371/journal.pcbi.0010075	2005
Metabolism	Characterization of the biosynthetic pathway of glucosylglycerate in the archaeon Methanococcoides burtonii.	Costa J, Empadinhas N, Goncalves L, Lamosa P, Santos H, da Costa MS.	J Bacteriol	10.1128/jb.188.3.1022-1030.2006	2006
	Noncoding RNA genes identified in AT-rich hyperthermophiles.	Klein RJ, Misulovin Z, Eddy SR.	Proc Natl Acad Sci U S A	10.1073/pnas.112063799	2002
Metabolism	A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes.	Haft DH, Selengut J, Mongodin EF, Nelson KE.	PLoS Comput Biol	10.1371/journal.pcbi.0010060	2005
Genetics	The cobweb of life revealed by genome-scale estimates of horizontal gene transfer.	Ge F, Wang LS, Kim J.	PLoS Biol	10.1371/journal.pbio.0030316	2005
	The complete genome sequence of Thermoproteus tenax: a physiologically versatile member of the Crenarchaeota.	Siebers B, Zaparty M, Raddatz G, Tjaden B, Albers SV, Bell SD, Blombach F, Kletzin A, Kyrpides N, Lanz C, Plagens A, Rampp M, Rosinus A, von Jan M, Makarova KS, Klenk HP, Schuster SC, Hensel R.	PLoS One	10.1371/journal.pone.0024222	2011
	Analysis of the first genome of a hyperthermophilic marine virus-like particle, PAV1, isolated from Pyrococcus abyssi.	Geslin C, Gaillard M, Flament D, Rouault K, Le Romancer M, Prieur D, Erauso G.	J Bacteriol	10.1128/jb.01896-06	2007
	Archaic chaos: intrinsically disordered proteins in Archaea.	Xue B, Williams RW, Oldfield CJ, Dunker AK, Uversky VN.	BMC Syst Biol	10.1186/1752-0509-4-s1-s1	2010
Metabolism	Structures of the signal recognition particle receptor from the archaeon Pyrococcus furiosus: implications for the targeting step at the membrane.	Egea PF, Tsuruta H, de Leon GP, Napetschnig J, Walter P, Stroud RM.	PLoS One	10.1371/journal.pone.0003619	2008
Enzymology	Orthologs of a novel archaeal and of the bacterial peptidyl-tRNA hydrolase are nonessential in yeast.	Rosas-Sandoval G, Ambrogelly A, Rinehart J, Wei D, Cruz-Vera LR, Graham DE, Stetter KO, Guarneros G, Soll D.	Proc Natl Acad Sci U S A	10.1073/pnas.222659199	2002
Phylogeny	Essential and non-essential DNA replication genes in the model halophilic Archaeon, Halobacterium sp. NRC-1.	Berquist BR, DasSarma P, DasSarma S.	BMC Genet	10.1186/1471-2156-8-31	2007
Genetics	Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale.	Lecompte O, Ripp R, Thierry JC, Moras D, Poch O.	Nucleic Acids Res	10.1093/nar/gkf693	2002
Phylogeny	Higher-level classification of the Archaea: evolution of methanogenesis and methanogens.	Bapteste E, Brochier C, Boucher Y.	Archaea	10.1155/2005/859728	2005
	A new computational method for the detection of horizontal gene transfer events.	Tsirigos A, Rigoutsos I.	Nucleic Acids Res	10.1093/nar/gki187	2005
	MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes.	Zhu H, Hu GQ, Yang YF, Wang J, She ZS.	BMC Bioinformatics	10.1186/1471-2105-8-97	2007
	A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities.	Bastien O, Ortet P, Roy S, Marechal E.	BMC Bioinformatics	10.1186/1471-2105-6-49	2005
	Prediction of signal recognition particle RNA genes.	Regalia M, Rosenblad MA, Samuelsson T.	Nucleic Acids Res	10.1093/nar/gkf468	2002
	Anisotropic solvent model of the lipid bilayer. 2. Energetics of insertion of small molecules, peptides, and proteins in membranes.	Lomize AL, Pogozheva ID, Mosberg HI.	J Chem Inf Model	10.1021/ci200020k	2011
	Identification and functional analysis of PCNA1 and PCNA-like1 genes of Phaseolus coccineus.	Strzalka W, Kaczmarek A, Naganowska B, Ziemienowicz A.	J Exp Bot	10.1093/jxb/erp354	2010
Enzymology	S-Adenosylmethionine decarboxylase from the archaeon Methanococcus jannaschii: identification of a novel family of pyruvoyl enzymes.	Kim AD, Graham DE, Seeholzer SH, Markham GD.	J Bacteriol	10.1128/jb.182.23.6667-6672.2000	2000
Metabolism	Biochemical characterization of Cdc6/Orc1 binding to the replication origin of the euryarchaeon Methanothermobacter thermoautotrophicus.	Capaldi SA, Berger JM.	Nucleic Acids Res	10.1093/nar/gkh819	2004
Genetics	Genomic context analysis in Archaea suggests previously unrecognized links between DNA replication and translation.	Berthon J, Cortez D, Forterre P.	Genome Biol	10.1186/gb-2008-9-4-r71	2008
	Expansion of protein domain repeats.	Bjorklund AK, Bjorklund AK, Ekman D, Elofsson A.	PLoS Comput Biol	10.1371/journal.pcbi.0020114	2006
Metabolism	The coiled-coil domain of the Nop56/58 core protein is dispensable for sRNP assembly but is critical for archaeal box C/D sRNP-guided nucleotide methylation.	Zhang X, Champion EA, Tran EJ, Brown BA, Baserga SJ, Maxwell ES.	RNA	10.1261/rna.2230106	2006
	Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases.	Taneja B, Patel A, Slesarev A, Mondragon A.	EMBO J	10.1038/sj.emboj.7600922	2006
Metabolism	Structural and biochemical basis for polyamine binding to the Tp0655 lipoprotein of Treponema pallidum: putative role for Tp0655 (TpPotD) as a polyamine receptor.	Machius M, Brautigam CA, Tomchick DR, Ward P, Otwinowski Z, Blevins JS, Deka RK, Norgard MV.	J Mol Biol	10.1016/j.jmb.2007.08.018	2007
Metabolism	DNA topoisomerase III from the hyperthermophilic archaeon Sulfolobus solfataricus with specific DNA cleavage activity.	Dai P, Wang Y, Ye R, Chen L, Huang L.	J Bacteriol	10.1128/jb.185.18.5500-5507.2003	2003
Metabolism	An unusual isopentenyl diphosphate isomerase found in the mevalonate pathway gene cluster from Streptomyces sp. strain CL190.	Kaneda K, Kuzuyama T, Takagi M, Hayakawa Y, Seto H.	Proc Natl Acad Sci U S A	10.1073/pnas.98.3.932	2001
Metabolism	Biochemical analysis of components of the pre-replication complex of Archaeoglobus fulgidus.	Grainge I, Scaife S, Wigley DB.	Nucleic Acids Res	10.1093/nar/gkg662	2003
Metabolism	Purification, overproduction, and partial characterization of beta-RFAP synthase, a key enzyme in the methanopterin biosynthesis pathway.	Scott JW, Rasche ME.	J Bacteriol	10.1128/jb.184.16.4442-4448.2002	2002
Enzymology	Bacteriophage T4 RNA ligase 2 (gp24.1) exemplifies a family of RNA ligases found in all phylogenetic domains.	Ho CK, Shuman S.	Proc Natl Acad Sci U S A	10.1073/pnas.192184699	2002
Metabolism	Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea.	de Crecy-Lagard V, Brochier-Armanet C, Urbonavicius J, Fernandez B, Phillips G, Lyons B, Noma A, Alvarez S, Droogmans L, Armengaud J, Grosjean H.	Mol Biol Evol	10.1093/molbev/msq096	2010
	The genomics of disulfide bonding and protein stabilization in thermophiles.	Beeby M, O'Connor BD, Ryttersgaard C, Boutz DR, Perry LJ, Yeates TO.	PLoS Biol	10.1371/journal.pbio.0030309	2005
Metabolism	Interactions between the archaeal Cdc6 and MCM proteins modulate their biochemical properties.	Kasiviswanathan R, Shin JH, Kelman Z.	Nucleic Acids Res	10.1093/nar/gki807	2005
Enzymology	A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya.	Kaya Y, Ofengand J.	RNA	10.1261/rna.5230603	2003
	Genetic and physical mapping of DNA replication origins in Haloferax volcanii.	Norais C, Hawkins M, Hartman AL, Eisen JA, Myllykallio H, Allers T.	PLoS Genet	10.1371/journal.pgen.0030077	2007
	Evolutionary rates vary among rRNA structural elements.	Smit S, Widmann J, Knight R.	Nucleic Acids Res	10.1093/nar/gkm101	2007
Genetics	The global intrinsic curvature of archaeal and eubacterial genomes is mostly contained in their dinucleotide composition and is probably not an adaptation.	Merino E, Garciarrubio A.	Nucleic Acids Res	10.1093/nar/28.12.2431	2000
	Gene fusions and gene duplications: relevance to genomic annotation and functional analysis.	Serres MH, Riley M.	BMC Genomics	10.1186/1471-2164-6-33	2005
	Ancient origin of the tryptophan operon and the dynamics of evolutionary change.	Xie G, Keyhani NO, Bonner CA, Jensen RA.	Microbiol Mol Biol Rev	10.1128/mmbr.67.3.303-342.2003	2003
Metabolism	Structure of an XPF endonuclease with and without DNA suggests a model for substrate recognition.	Newman M, Murray-Rust J, Lally J, Rudolf J, Fadden A, Knowles PP, White MF, McDonald NQ.	EMBO J	10.1038/sj.emboj.7600581	2005
Metabolism	Posttranslational protein modification in Archaea.	Eichler J, Adams MW, Adams MW.	Microbiol Mol Biol Rev	10.1128/mmbr.69.3.393-425.2005	2005
Metabolism	Truncation analysis of TatA and TatB defines the minimal functional units required for protein translocation.	Lee PA, Buchanan G, Stanley NR, Berks BC, Palmer T.	J Bacteriol	10.1128/jb.184.21.5871-5879.2002	2002
Genetics	Computational identification of operons in microbial genomes.	Zheng Y, Szustakowski JD, Fortnow L, Roberts RJ, Kasif S.	Genome Res	10.1101/gr.200602	2002
Genetics	Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response.	Becker EA, Seitzer PM, Tritt A, Larsen D, Krusor M, Yao AI, Wu D, Madern D, Eisen JA, Darling AE, Facciotti MT.	PLoS Genet	10.1371/journal.pgen.1004784	2014
Metabolism	Crystal structures of Escherichia coli ATP-dependent glucokinase and its complex with glucose.	Lunin VV, Li Y, Schrag JD, Iannuzzi P, Cygler M, Matte A.	J Bacteriol	10.1128/jb.186.20.6915-6927.2004	2004
	A Holliday junction resolvase from Pyrococcus furiosus: functional similarity to Escherichia coli RuvC provides evidence for conserved mechanism of homologous recombination in Bacteria, Eukarya, and Archaea.	Komori K, Sakae S, Shinagawa H, Morikawa K, Ishino Y.	Proc Natl Acad Sci U S A	10.1073/pnas.96.16.8873	1999
Metabolism	Identification of Streptococcus thermophilus CNRZ368 genes involved in defense against superoxide stress.	Thibessard A, Borges F, Fernandez A, Gintz B, Decaris B, Leblond-Bourget N.	Appl Environ Microbiol	10.1128/aem.70.4.2220-2229.2004	2004
Genetics	Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.	Marsden RL, Lee D, Maibaum M, Yeats C, Orengo CA.	Nucleic Acids Res	10.1093/nar/gkj494	2006
	Two novel families of plasmids from hyperthermophilic archaea encoding new families of replication proteins.	Soler N, Marguet E, Cortez D, Desnoues N, Keller J, van Tilbeurgh H, Sezonov G, Forterre P.	Nucleic Acids Res	10.1093/nar/gkq236	2010
Enzymology	Glycerate kinase of the hyperthermophilic archaeon Thermoproteus tenax: new insights into the phylogenetic distribution and physiological role of members of the three different glycerate kinase classes.	Kehrer D, Ahmed H, Brinkmann H, Siebers B.	BMC Genomics	10.1186/1471-2164-8-301	2007
Enzymology	Cold and Hot Extremozymes: Industrial Relevance and Current Trends.	Sarmiento F, Peralta R, Blamey JM.	Front Bioeng Biotechnol	10.3389/fbioe.2015.00148	2015
Pathogenicity	Occurrence and characterization of mercury resistance in the hyperthermophilic archaeon Sulfolobus solfataricus by use of gene disruption.	Schelert J, Dixit V, Hoang V, Simbahan J, Drozda M, Blum P.	J Bacteriol	10.1128/jb.186.2.427-437.2004	2004
	Refuting phylogenetic relationships.	Bucknam J, Boucher Y, Bapteste E.	Biol Direct	10.1186/1745-6150-1-26	2006
Genetics	Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence.	Kennedy SP, Ng WV, Salzberg SL, Hood L, DasSarma S.	Genome Res	10.1101/gr.190201	2001
	Substrate recognition by class I lysyl-tRNA synthetases: a molecular basis for gene displacement.	Ibba M, Losey HC, Kawarabayasi Y, Kikuchi H, Bunjun S, Soll D.	Proc Natl Acad Sci U S A	10.1073/pnas.96.2.418	1999
	Comparative analysis of protein domain organization.	Ye Y, Godzik A.	Genome Res	10.1101/gr.1610504	2004
Enzymology	Structural and biochemical characterization of peroxiredoxin Qbeta from Xylella fastidiosa: catalytic mechanism and high reactivity.	Horta BB, de Oliveira MA, Discola KF, Cussiol JR, Netto LE.	J Biol Chem	10.1074/jbc.m109.094839	2010
Enzymology	Characterization of an aminoacylase from the hyperthermophilic archaeon Pyrococcus furiosus.	Story SV, Grunden AM, Adams MW, Adams MW.	J Bacteriol	10.1128/jb.183.14.4259-4268.2001	2001
Metabolism	The Cm56 tRNA modification in archaea is catalyzed either by a specific 2'-O-methylase, or a C/D sRNP.	Renalier MH, Joseph N, Gaspin C, Thebault P, Mougin A.	RNA	10.1261/rna.2110805	2005
Phylogeny	Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ.	Omelchenko MV, Makarova KS, Wolf YI, Rogozin IB, Koonin EV.	Genome Biol	10.1186/gb-2003-4-9-r55	2003
Genetics	Genomics of an extreme psychrophile, Psychromonas ingrahamii.	Riley M, Staley JT, Danchin A, Wang TZ, Brettin TS, Hauser LJ, Land ML, Thompson LS.	BMC Genomics	10.1186/1471-2164-9-210	2008
Metabolism	A recurrent general RNA binding domain appended to plant methionyl-tRNA synthetase acts as a cis-acting cofactor for aminoacylation.	Kaminska M, Deniziak M, Kerjan P, Barciszewski J, Mirande M.	EMBO J	10.1093/emboj/19.24.6908	2000
Metabolism	Metabolism of halophilic archaea.	Falb M, Muller K, Konigsmaier L, Oberwinkler T, Horn P, von Gronau S, Gonzalez O, Pfeiffer F, Bornberg-Bauer E, Oesterhelt D.	Extremophiles	10.1007/s00792-008-0138-x	2008
	Molecular dynamics simulations of voltage-gated cation channels: insights on voltage-sensor domain function and modulation.	Delemotte L, Klein ML, Tarek M.	Front Pharmacol	10.3389/fphar.2012.00097	2012
Genetics	Detection and characterization of horizontal transfers in prokaryotes using genomic signature.	Dufraigne C, Fertil B, Lespinats S, Giron A, Deschavanne P.	Nucleic Acids Res	10.1093/nar/gni004	2005
	Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea.	Rodionov DA, Mironov AA, Gelfand MS.	Genome Res	10.1101/gr.314502	2002
Enzymology	Activation mutants in yeast RNA polymerase II subunit RPB3 provide evidence for a structurally conserved surface required for activation in eukaryotes and bacteria.	Tan Q, Linask KL, Ebright RH, Woychik NA.	Genes Dev	10.1101/gad.14.3.339	2000
Metabolism	Peptidase E, a peptidase specific for N-terminal aspartic dipeptides, is a serine hydrolase.	Lassy RA, Miller CG.	J Bacteriol	10.1128/jb.182.9.2536-2543.2000	2000
Genetics	Connected gene neighborhoods in prokaryotic genomes.	Rogozin IB, Makarova KS, Murvai J, Czabarka E, Wolf YI, Tatusov RL, Szekely LA, Koonin EV.	Nucleic Acids Res	10.1093/nar/30.10.2212	2002
Metabolism	Assembly of archaeal signal recognition particle from recombinant components.	Bhuiyan SH, Gowda K, Hotokezaka H, Zwieb C.	Nucleic Acids Res	10.1093/nar/28.6.1365	2000
	Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.	Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J.	Genome Res	10.1101/gr.1993504	2004
Genetics	A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis.	Makarova KS, Aravind L, Grishin NV, Rogozin IB, Koonin EV.	Nucleic Acids Res	10.1093/nar/30.2.482	2002
Metabolism	Convergence and constraint in eukaryotic release factor 1 (eRF1) domain 1: the evolution of stop codon specificity.	Inagaki Y, Blouin C, Doolittle WF, Roger AJ.	Nucleic Acids Res	10.1093/nar/30.2.532	2002
	A census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial IQ, extroverts and introverts.	Galperin MY.	BMC Microbiol	10.1186/1471-2180-5-35	2005
Metabolism	Box C/D RNA guides for the ribose methylation of archaeal tRNAs. The tRNATrp intron guides the formation of two ribose-methylated nucleosides in the mature tRNATrp.	Clouet d'Orval B, Bortolin ML, Gaspin C, Bachellerie JP.	Nucleic Acids Res	10.1093/nar/29.22.4518	2001
	A homology model of the pore region of HCN channels.	Giorgetti A, Carloni P, Mistrik P, Torre V.	Biophys J	10.1529/biophysj.104.045286	2005
Metabolism	Conversion of methionine to cysteine in Bacillus subtilis and its regulation.	Hullo MF, Auger S, Soutourina O, Barzu O, Yvon M, Danchin A, Martin-Verstraete I.	J Bacteriol	10.1128/jb.01273-06	2007
Genetics	Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes.	Fukui T, Atomi H, Kanai T, Matsumi R, Fujiwara S, Imanaka T.	Genome Res	10.1101/gr.3003105	2005
Metabolism	Biochemical analysis of replication factor C from the hyperthermophilic archaeon Pyrococcus furiosus.	Cann IK, Ishino S, Yuasa M, Daiyasu H, Toh H, Ishino Y.	J Bacteriol	10.1128/jb.183.8.2614-2623.2001	2001
	The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments.	Gonzalez V, Bustos P, Ramirez-Romero MA, Medrano-Soto A, Salgado H, Hernandez-Gonzalez I, Hernandez-Celis JC, Quintero V, Moreno-Hagelsieb G, Girard L, Rodriguez O, Flores M, Cevallos MA, Collado-Vides J, Romero D, Davila G.	Genome Biol	10.1186/gb-2003-4-6-r36	2003
	Coupled motions between pore and voltage-sensor domains: a model for Shaker B, a voltage-gated potassium channel.	Treptow W, Maigret B, Chipot C, Tarek M.	Biophys J	10.1529/biophysj.104.039628	2004
	Detection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase superfamily.	Mazumder R, Iyer LM, Vasudevan S, Aravind L.	Nucleic Acids Res	10.1093/nar/gkf645	2002
	PSI-BLAST searches using hidden markov models of structural repeats: prediction of an unusual sliding DNA clamp and of beta-propellers in UV-damaged DNA-binding protein.	Neuwald AF, Poleksic A.	Nucleic Acids Res	10.1093/nar/28.18.3570	2000
Phylogeny	Evolutionary appearance of genes encoding proteins associated with box H/ACA snoRNAs: cbf5p in Euglena gracilis, an early diverging eukaryote, and candidate Gar1p and Nop10p homologs in archaebacteria.	Watanabe Y, Gray MW.	Nucleic Acids Res	10.1093/nar/28.12.2342	2000
Metabolism	Functional interactions of a homolog of proliferating cell nuclear antigen with DNA polymerases in Archaea.	Cann IK, Ishino S, Hayashi I, Komori K, Toh H, Morikawa K, Ishino Y.	J Bacteriol	10.1128/jb.181.21.6591-6599.1999	1999
	Electrostatic model of S4 motion in voltage-gated ion channels.	Lecar H, Larsson HP, Grabe M.	Biophys J	10.1016/s0006-3495(03)74708-0	2003
Genetics	A complete sequence of the T. tengcongensis genome.	Bao Q, Tian Y, Li W, Xu Z, Xuan Z, Hu S, Dong W, Yang J, Chen Y, Xue Y, Xu Y, Lai X, Huang L, Dong X, Ma Y, Ling L, Tan H, Chen R, Wang J, Yu J, Yang H.	Genome Res	10.1101/gr.219302	2002
	An inventory of yeast proteins associated with nucleolar and ribosomal components.	Staub E, Mackowiak S, Vingron M.	Genome Biol	10.1186/gb-2006-7-10-r98	2006
	Structural characterization of the human proteome.	Muller A, MacCallum RM, Sternberg MJ.	Genome Res	10.1101/gr.221202	2002
Genetics	A Meier-Gorlin syndrome mutation in a conserved C-terminal helix of Orc6 impedes origin recognition complex formation.	Bleichert F, Balasov M, Chesnokov I, Nogales E, Botchan MR, Berger JM.	Elife	10.7554/elife.00882	2013
	Biosynthesis and role of N-linked glycosylation in cell surface structures of archaea with a focus on flagella and s layers.	Jarrell KF, Jones GM, Nair DB.	Int J Microbiol	10.1155/2010/470138	2010
	SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories.	Aravind L, Makarova KS, Koonin EV.	Nucleic Acids Res	10.1093/nar/28.18.3417	2000
Phylogeny	Genome trees constructed using five different approaches suggest new major bacterial clades.	Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, Koonin EV.	BMC Evol Biol	10.1186/1471-2148-1-8	2001
Metabolism	The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis.	Fricke WF, Seedorf H, Henne A, Kruer M, Liesegang H, Hedderich R, Gottschalk G, Thauer RK.	J Bacteriol	10.1128/jb.188.2.642-658.2006	2006
Metabolism	Chemoenzymatic Semisynthesis of Proteins.	Thompson RE, Muir TW.	Chem Rev	10.1021/acs.chemrev.9b00450	2020
Metabolism	Aminoacyl-tRNA Synthetases in the Bacterial World.	Giege R, Springer M.	EcoSal Plus	10.1128/ecosalplus.esp-0002-2016	2016
Metabolism	Comparative genomics and evolution of proteins involved in RNA metabolism.	Anantharaman V, Koonin EV, Aravind L.	Nucleic Acids Res	10.1093/nar/30.7.1427	2002
Metabolism	Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation.	Brasen C, Esser D, Rauch B, Siebers B.	Microbiol Mol Biol Rev	10.1128/mmbr.00041-13	2014
	Molecular diversity and regulation of renal potassium channels.	Hebert SC, Desir G, Giebisch G, Wang W.	Physiol Rev	10.1152/physrev.00051.2003	2005
Enzymology	Kinetic study of sn-glycerol-1-phosphate dehydrogenase from the aerobic hyperthermophilic archaeon, Aeropyrum pernix K1.	Han JS, Kosugi Y, Ishida H, Ishikawa K	Eur J Biochem	10.1046/j.0014-2956.2001.02731.x	2002
Enzymology	Glutamate dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix K1: enzymatic characterization, identification of the encoding gene, and phylogenetic implications.	Bhuiya MW, Sakuraba H, Kujo C, Nunoura-Kominato N, Kawarabayasi Y, Kikuchi H, Ohshima T	Extremophiles	10.1007/s007920070002	2000
Enzymology	Purification and characterization of an intracellular heat-stable proteinase (pernilase) from the marine hyperthermophilic archaeon Aeropyrum pernix K1.	Chavez Croocker P, Sako Y, Uchida A	Extremophiles	10.1007/s007920050093	1999
Enzymology	An extremely heat-stable extracellular proteinase (aeropyrolysin) from the hyperthermophilic archaeon Aeropyrum pernix K1.	Sako Y, Croocker PC, Ishida Y	FEBS Lett	10.1016/s0014-5793(97)01153-8	1997
	Pyrobaculum calidifontis sp. nov., a novel hyperthermophilic archaeon that grows in atmospheric air.	Amo T, Paje ML, Inagaki A, Ezaki S, Atomi H, Imanaka T.	Archaea	10.1155/2002/616075	2002
Phylogeny	Aeropyrum pernix gen. nov., sp. nov., a novel aerobic hyperthermophilic archaeon growing at temperatures up to 100 degrees C.	Sako Y, Nomura N, Uchida A, Ishida Y, Morii H, Koga Y, Hoaki T, Maruyama T	Int J Syst Bacteriol	10.1099/00207713-46-4-1070	1996

References

#4521	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 11879
#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#23222	YOSHIHIKO SAKO, NORIMICHI NOMURA, ARITSUNE UCHIDA, YUZABURO ISHIDA, HIROYUKI MORII, YOSUKE KOGA, TOSHIHIRO HOAKI, TADASHI MARUYAMA: Aeropyrum pernix gen. nov., sp. nov., a Novel Aerobic Hyperthermophilic Archaeon Growing at Temperatures up to 100°C. IJSEM 46: 1070 - 1077 1996 ( DOI 10.1099/00207713-46-4-1070 , PubMed 8863437 )
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Aeropyrum pernix (DSM 11879, JCM 9820, K1)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

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Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

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Genome sequences

Genome browser: GCA_000011125

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