Strain identifier

BacDive ID: 4163

Type strain: No

Species: Nitratidesulfovibrio vulgaris

Strain Designation: Miyazaki F

Strain history: H. Akutsu <-- S. Iwasaki strain Miyazaki F.

NCBI tax ID(s): 881 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 8227

BacDive-ID: 4163

DSM-Number: 19637

keywords: genome sequence, Bacteria, anaerobe, mesophilic

description: Nitratidesulfovibrio vulgaris Miyazaki F is an anaerobe, mesophilic bacterium that was isolated from degraded paddy field.

NCBI tax id

  • NCBI tax id: 881
  • Matching level: species

strain history

@refhistory
8227<- J.D. Wall <- H. Akutso, Yokohama National University <- Osaka University <- Tokyo University <- Ajinomoto Co. Inc.; Miyazaki F {1949}
67770H. Akutsu <-- S. Iwasaki strain Miyazaki F.

doi: 10.13145/bacdive4163.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Desulfovibrionales
  • family: Desulfovibrionaceae
  • genus: Nitratidesulfovibrio
  • species: Nitratidesulfovibrio vulgaris
  • full scientific name: Nitratidesulfovibrio vulgaris (Postgate and Campbell 1966) Waite et al. 2020
  • synonyms

    • @ref: 20215
    • synonym: Desulfovibrio vulgaris

@ref: 8227

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfovibrionales

family: Desulfovibrionaceae

genus: Desulfovibrio

species: Desulfovibrio vulgaris

full scientific name: Desulfovibrio vulgaris Postgate and Campbell 1966

strain designation: Miyazaki F

type strain: no

Culture and growth conditions

culture medium

  • @ref: 8227
  • name: DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/641
  • composition: Name: DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641) Composition: Na-DL-lactate 2.49252 g/l Na2SO4 1.99402 g/l NH4Cl 0.997009 g/l Yeast extract 0.997009 g/l Na2CO3 0.997009 g/l MgSO4 x 7 H2O 0.997009 g/l Na2S2O3 x 5 H2O 0.997009 g/l KH2PO4 0.498504 g/l Na2S x 9 H2O 0.0997009 g/l CaCl2 x 2 H2O 0.0997009 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Pyridoxine hydrochloride 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
8227positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 8227
  • oxygen tolerance: anaerobe

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8227degraded paddy fieldMiyazakiJapanJPNAsia
67770Paddy field soil in MiyazakiJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Mud (Sludge)

Safety information

risk assessment

  • @ref: 8227
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

  • @ref: 66792
  • description: Desulfovibrio vulgaris Miyazaki F
  • accession: 643348539
  • assembly level: complete
  • database: img
  • NCBI tax ID: 883

GC content

  • @ref: 8227
  • GC-content: 67
  • method: sequence analysis

External links

@ref: 8227

culture collection no.: DSM 19637, JCM 14930

straininfo link

  • @ref: 73664
  • straininfo: 402991

literature

topicPubmed-IDtitleauthorsjournalyearmeshDOItopic2
Phylogeny479126Crystallographic data for cytochrome c3 from two strains of Desulfovibrio vulgaris, Miyazaki.Bando S, Matsuura Y, Tanaka N, Yasuoka N, Kakudo M, Yagi T, Inokuchi HJ Biochem1979*Cytochromes, Desulfovibrio/*analysis, Protein Conformation, Species Specificity, X-Ray Diffraction
Enzymology1332780Reduction kinetics of the four hemes of cytochrome c3 from Desulfovibrio vulgaris by flash photolysis.Akutsu H, Hazzard JH, Bartsch RG, Cusanovich MABiochim Biophys Acta1992Cytochrome c Group/*chemistry/isolation & purification, Desulfovibrio vulgaris/*enzymology, Edetic Acid, Heme/chemistry, Hydrogen-Ion Concentration, Kinetics, Oxidation-Reduction10.1016/0005-2728(92)90003-kPhylogeny
1333991Assignment of the redox potentials to the four haems in Desulfovibrio vulgaris cytochrome c3 by 2D-NMR.Salgueiro CA, Turner DL, Santos H, LeGall J, Xavier AVFEBS Lett1992Cytochrome c Group/*chemistry, Desulfovibrio vulgaris/*chemistry, Heme/*chemistry, Magnetic Resonance Spectroscopy/methods, Oxidation-Reduction, Structure-Activity Relationship, X-Ray Diffraction10.1016/0014-5793(92)80963-h
Metabolism1336461Structural studies of Desulfovibrio vulgaris ferrocytochrome c3 by two-dimensional NMR.Turner DL, Salgueiro CA, LeGall J, Xavier AVEur J Biochem1992Amino Acid Sequence, Cytochrome c Group/*chemistry, Desulfovibrio vulgaris/*metabolism, Heme/analysis, Magnetic Resonance Spectroscopy/methods, Models, Molecular, Protein Conformation10.1111/j.1432-1033.1992.tb17497.x
Metabolism16687231H NMR studies on ferricytochrome c3 from Desulfovibrio vulgaris Miyazaki F and its interaction with ferredoxin I.Park JS, Kano K, Morimoto Y, Higuchi Y, Yasuoka N, Ogata M, Niki K, Akutsu HJ Biomol NMR1991Binding Sites, Cytochrome c Group/chemistry/*metabolism, Desulfovibrio vulgaris/*metabolism, Ferredoxins/chemistry/*metabolism, Heme/metabolism, Hydrogen, Kinetics, Magnetic Resonance Spectroscopy/methods, Oxidation-Reduction, Protein Binding, Protein Conformation10.1007/BF01875520Enzymology
Phylogeny1964450S-class cytochromes c have a variety of folding patterns: structure of cytochrome c-553 from Desulfovibrio vulgaris determined by the multi-wavelength anomalous dispersion method.Nakagawa A, Higuchi Y, Yasuoka N, Katsube Y, Yagi TJ Biochem1990Amino Acid Sequence, Cytochrome c Group/*chemistry/classification/genetics, Desulfovibrio/*enzymology/genetics, Molecular Sequence Data, Phylogeny, Protein Conformation, X-Ray Diffraction10.1093/oxfordjournals.jbchem.a123267Genetics
Enzymology2081730Redox process of iron-sulfur clusters of the soluble-domain of the membrane-bound hydrogenase from Desulfovibrio vulgaris Miyazaki F studied by resonance Raman spectroscopy.Furuichi H, Ozaki Y, Niki K, Akutsu HJ Biochem1990Binding Sites, Cluster Analysis, Desulfovibrio/*enzymology, Iron/chemistry/*metabolism, Oxidation-Reduction, Oxidoreductases/chemistry/*metabolism, Solubility, Spectrum Analysis, Raman, Sulfur/chemistry/*metabolism10.1093/oxfordjournals.jbchem.a123269Metabolism
Metabolism2159795Estimation of microscopic redox potentials of a tetraheme protein, cytochrome c3 of Desulfovibrio vulgaris, Miyazaki F, and partial assignments of heme groups.Fan KJ, Akutsu H, Kyogoku Y, Niki KBiochemistry1990Cytochrome c Group/*metabolism, Desulfovibrio/*enzymology, *Heme, Magnetic Resonance Spectroscopy, Oxidation-Reduction10.1021/bi00461a008Enzymology
Enzymology2269874Cloning and sequencing of a [NiFe] hydrogenase operon from Desulfovibrio vulgaris Miyazaki F.Deckers HM, Wilson FR, Voordouw GJ Gen Microbiol1990Amino Acid Sequence, Base Sequence, Cloning, Molecular, DNA, Bacterial/genetics, Desulfovibrio/*enzymology/genetics, Genes, Bacterial, Hydrogenase/*genetics, Molecular Sequence Data, Operon, Restriction Mapping, Sequence Homology, Nucleic Acid10.1099/00221287-136-10-2021Genetics
Enzymology2987196Analysis of the active center of hydrogenase from Desulfovibrio vulgaris Miyazaki by magnetic measurements.Yagi T, Kimura K, Inokuchi HJ Biochem1985Desulfovibrio/*enzymology, Electron Spin Resonance Spectroscopy, Ferricyanides/pharmacology, Hydrogenase/*analysis, Iron/analysis, Microwaves, Nickel/analysis, Spectrometry, Gamma, Temperature, Zinc/analysis10.1093/oxfordjournals.jbchem.a135042
Enzymology2993256Purification and properties of thiosulfate reductase from Desulfovibrio vulgaris, Miyazaki F.Aketagawa J, Kobayashi K, Ishimoto MJ Biochem1985Cytochrome c Group/metabolism, Desulfovibrio/*enzymology, Hydrogen-Ion Concentration, Iron/metabolism, Molecular Weight, Oxidation-Reduction, Oxidoreductases/*isolation & purification/metabolism, Oxidoreductases Acting on Sulfur Group Donors, Spectrum Analysis, Sulfurtransferases10.1093/oxfordjournals.jbchem.a135144Metabolism
Metabolism3023304Pyruvate dehydrogenase and the path of lactate degradation in Desulfovibrio vulgaris Miyazaki F.Ogata M, Yagi TJ Biochem1986Acetyl Coenzyme A/metabolism, Cytochrome c Group/metabolism, Desulfovibrio/*enzymology, Flavin Mononucleotide/metabolism, Hydrogen-Ion Concentration, Ketone Oxidoreductases/metabolism, Kinetics, Lactates/*metabolism, Lactic Acid, Molecular Weight, Pyruvate Dehydrogenase Complex/*metabolism, Pyruvate Synthase, Pyruvates/metabolism, Pyruvic Acid, Substrate Specificity, Temperature10.1093/oxfordjournals.jbchem.a121717Enzymology
Enzymology3546297Single crystals of hydrogenase from Desulfovibrio vulgaris Miyazaki F.Higuchi Y, Yasuoka N, Kakudo M, Katsube Y, Yagi T, Inokuchi HJ Biol Chem1987Chromatography, High Pressure Liquid, Crystallization, Desulfovibrio/*enzymology, Diffusion, Glycols, *Hydrogenase, Polyethylene GlycolsS0021-9258(18)61580-7
Enzymology3897216Magnetic susceptibility of hydrogenase from Desulfovibrio vulgaris.Kimura K, Inokuchi H, Nanami H, Yagi TJ Biochem1985Desulfovibrio/*enzymology, Hydrogenase/*analysis, Iron-Sulfur Proteins/analysis, Magnetics, Models, Chemical, Temperature10.1093/oxfordjournals.jbchem.a135246
Enzymology6874662Characterization of periplasmic hydrogenase from Desulfovibrio vulgaris Miyazaki K.Aketagawa J, Kobayashi K, Ishimoto MJ Biochem1983Amino Acids/analysis, Chemical Phenomena, Chemistry, Desulfovibrio/*enzymology, Immunochemistry, Molecular Weight, Oxidoreductases/*isolation & purification10.1093/jb/93.3.755Phylogeny
Enzymology7548038Structure of the tetraheme cytochrome from Desulfovibrio desulfuricans ATCC 27774: X-ray diffraction and electron paramagnetic resonance studies.Morais J, Palma PN, Frazao C, Caldeira J, LeGall J, Moura I, Moura JJ, Carrondo MABiochemistry1995Crystallography, X-Ray, Cytochrome c Group/*chemistry, Desulfovibrio/*enzymology, Electron Spin Resonance Spectroscopy, Hydrogen Bonding, Models, Molecular, Oxidation-Reduction, Protein Conformation10.1021/bi00039a044
Enzymology7783682A gene encoding a cytochrome c oxidase-like protein is located closely to the cytochrome c-553 gene in the anaerobic bacterium, Desulfovibrio vulgaris (Miyazaki F).Kitamura M, Mizugai K, Taniguchi M, Akutsu H, Kumagai I, Nakaya TMicrobiol Immunol1995Amino Acid Sequence, Base Sequence, Cloning, Molecular, Cytochrome c Group/*genetics, Desulfovibrio vulgaris/enzymology/*genetics, Electron Transport Complex IV/*genetics, Genes, Bacterial/*genetics, Molecular Sequence Data, Protein Sorting Signals/genetics, Sequence Analysis, DNA, Sequence Homology, Amino Acid10.1111/j.1348-0421.1995.tb02172.xGenetics
Enzymology8119891Novel FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F). Cloning and expression of its gene in Escherichia coli.Kitamura M, Kojima S, Ogasawara K, Nakaya T, Sagara T, Niki K, Miura K, Akutsu H, Kumagai IJ Biol Chem1994Amino Acid Sequence, Bacterial Proteins/*genetics/metabolism, Base Sequence, Blotting, Western, Carrier Proteins/*genetics/metabolism, Chromatography, High Pressure Liquid, Chromatography, Ion Exchange, Cloning, Molecular, DNA, Bacterial, Desulfovibrio vulgaris/*genetics/metabolism, Electrochemistry, Electrophoresis, Polyacrylamide Gel, Escherichia coli, Flavin Mononucleotide/*metabolism, *Flavoproteins, Genes, Bacterial, Molecular Sequence Data, Oxidation-ReductionS0021-9258(17)37499-9Metabolism
Metabolism8254667Structure analysis of cytochrome c3 from Desulfovibrio vulgaris Hildenborough at 1.9 A resolution.Matias PM, Frazao C, Morais J, Coll M, Carrondo MAJ Mol Biol1993Amino Acid Sequence, Cytochrome c Group/*chemistry/metabolism, Desulfovibrio vulgaris/*metabolism, Heme/analysis, Models, Structural, Molecular Sequence Data, Molecular Weight, Oxidation-Reduction, *Protein Conformation, Sequence Homology, Amino Acid, Solvents, X-Ray Diffraction/methods10.1006/jmbi.1993.1620Genetics
Enzymology9116039Cloning and expression of the rubredoxin gene from Desulfovibrio vulgaris (Miyazaki F)--comparison of the primary structure of desulfoferrodoxin.Kitamura M, Koshino Y, Kamikawa Y, Kohno K, Kojima S, Miura K, Sagara T, Akutsu H, Kumagai I, Nakaya TBiochim Biophys Acta1997Amino Acid Sequence, Base Sequence, Cloning, Molecular, Desulfovibrio vulgaris/*genetics, Electron Spin Resonance Spectroscopy, Escherichia coli/genetics, Ferredoxins/genetics, *Genes, Bacterial, Genetic Vectors, Iron/analysis, Molecular Sequence Data, NADH, NADPH Oxidoreductases/metabolism, Recombinant Proteins/biosynthesis/isolation & purification, Restriction Mapping, Rubredoxins/biosynthesis/*genetics/isolation & purification, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Spectrophotometry, Zinc/analysis10.1016/s0167-4781(96)00203-5Genetics
Enzymology9562622Cloning and expression of the gene encoding flavodoxin from Desulfovibrio vulgaris (Miyazaki F).Kitamura M, Sagara T, Taniguchi M, Ashida M, Ezoe K, Kohno K, Kojima S, Ozawa K, Akutsu H, Kumagai I, Nakaya TJ Biochem1998Base Sequence, *Cloning, Molecular, Desulfovibrio vulgaris/*genetics, Electrochemistry, Electrodes, Electrophoresis, Polyacrylamide Gel, Escherichia coli/metabolism, Flavin Mononucleotide/metabolism, Flavodoxin/*biosynthesis/chemistry/genetics/isolation & purification, *Gene Expression, *Genes, Bacterial, Graphite, Immunoblotting, Molecular Sequence Data, Mutagenesis, Site-Directed, Oxidation-Reduction, Protein Binding, Recombinant Proteins/chemistry/genetics/isolation & purification, Spectrophotometry, Ultraviolet10.1093/oxfordjournals.jbchem.a022021Metabolism
Metabolism9726950Ionic strength-dependent physicochemical factors in cytochrome c3 regulating the electron transfer rate.Ohmura T, Nakamura H, Niki K, Cusanovich MA, Akutsu HBiophys J1998Biophysical Phenomena, Biophysics, Chemical Phenomena, Chemistry, Physical, Cytochrome c Group/*chemistry/*metabolism, Desulfovibrio vulgaris/metabolism, Electron Transport, Heme/chemistry, Histidine/chemistry, Kinetics, Magnetic Resonance Spectroscopy, Osmolar Concentration, Oxidation-Reduction, Static Electricity10.1016/S0006-3495(98)74067-6Enzymology
Genetics10089348Structure determination of rubredoxin from Desulfovibrio vulgaris Miyazaki F in two crystal forms.Misaki S, Morimoto Y, Ogata M, Yagi T, Higuchi Y, Yasuoka NActa Crystallogr D Biol Crystallogr1999Amino Acid Sequence, Crystallography, X-Ray, Desulfovibrio vulgaris/*chemistry, Iron/chemistry, Models, Molecular, Molecular Sequence Data, Protein Conformation, Rubredoxins/*chemistry, Sequence Homology, Amino Acid10.1107/s0907444998011810
Metabolism10216314Crystallization and preliminary crystallographic studies of FMN-binding protein from Desulfovibrio vulgaris miyazaki F.Suto K, Kawagoe K, Shibata N, Morimoto Y, Higuchi Y, Kitamura M, Nakaya T, Yasuoka NActa Crystallogr D Biol Crystallogr1999Bacterial Proteins/*chemistry, Carrier Proteins/*chemistry, Crystallization, Crystallography, X-Ray, Desulfovibrio vulgaris/*chemistry, Flavin Mononucleotide/*metabolism, *Flavoproteins, Protein Conformation10.1107/s0907444999003169
Metabolism10378274Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution.Higuchi Y, Ogata H, Miki K, Yasuoka N, Yagi TStructure1999Binding Sites, Crystallography, X-Ray, Hydrogen/*chemistry, Hydrogenase/*chemistry/metabolism, Iron/*metabolism, Ligands, Models, Molecular, Nickel/*metabolism, Protein Conformation10.1016/s0969-2126(99)80071-9Enzymology
10713530How do the x-ray structure and the NMR structure of FMN-binding protein differ?Suto K, Kawagoe K, Shibata N, Morimoto Y, Higuchi Y, Kitamura M, Nakaya T, Yasuoka NActa Crystallogr D Biol Crystallogr2000Bacterial Proteins/*chemistry, Carrier Proteins/*chemistry, Crystallization, Crystallography, X-Ray, Desulfovibrio vulgaris/*chemistry, Dimerization, *Flavoproteins, Magnetic Resonance Spectroscopy, Models, Molecular, Protein Conformation, Solvents, Xylenes10.1107/s0907444900000111
Enzymology10735863Evidence for the presence of an F-type ATP synthase involved in sulfate respiration in Desulfovibrio vulgaris.Ozawa K, Meikari T, Motohashi K, Yoshida M, Akutsu HJ Bacteriol2000Amino Acid Sequence, Base Sequence, Cloning, Molecular, Desulfovibrio vulgaris/enzymology/*genetics, Electron Transport, Genes, Bacterial, Molecular Sequence Data, Open Reading Frames, Proton-Translocating ATPases/*genetics/isolation & purification, Sulfates/*metabolism10.1128/JB.182.8.2200-2206.2000Genetics
Enzymology10766434Single crystal EPR studies of the oxidized active site of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F.Trofanchuk O, Stein M, Gessner C, Lendzian F, Higuchi Y, Lubitz WJ Biol Inorg Chem2000Binding Sites, Desulfovibrio vulgaris/*enzymology, Electron Spin Resonance Spectroscopy/*methods, Hydrogenase/*chemistry/metabolism, Models, Molecular, Protein Conformation10.1007/pl00010654Metabolism
Metabolism10966450Expression of a tetraheme protein, Desulfovibrio vulgaris Miyazaki F cytochrome c(3), in Shewanella oneidensis MR-1.Ozawa K, Tsapin AI, Nealson KH, Cusanovich MA, Akutsu HAppl Environ Microbiol2000Aerobiosis, Anaerobiosis, Cytochrome c Group/chemistry/*genetics/*metabolism, Desulfovibrio vulgaris/genetics/*metabolism, Plasmids/genetics, Recombinant Proteins/chemistry/metabolism, Shewanella/*genetics/growth & development/metabolism10.1128/AEM.66.9.4168-4171.2000
Enzymology11001090The presence of a SO molecule in [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki as detected by mass spectrometry.Higuchi Y, Toujou F, Tsukamoto K, Yagi TJ Inorg Biochem2000Desulfovibrio vulgaris/chemistry/*enzymology, Hydrogenase/*chemistry/isolation & purification, Mass Spectrometry/*methods, Molecular Structure, Protein Denaturation, Spectroscopy, Fourier Transform Infrared, Sulfur Oxides/*chemistry10.1016/s0162-0134(00)00081-7Phylogeny
Enzymology11226874Cloning and expression of the catalase gene from the anaerobic bacterium Desulfovibrio vulgaris (Miyazaki F).Kitamura M, Nakanishi T, Kojima S, Kumagai I, Inoue HJ Biochem2001Amino Acid Sequence, Base Sequence, Blotting, Western, Catalase/chemistry/*genetics/metabolism, Chromatography, High Pressure Liquid, Cloning, Molecular, Desulfovibrio vulgaris/*enzymology/genetics, Electrophoresis, Polyacrylamide Gel, Escherichia coli, Heme/metabolism, Holoenzymes/chemistry/genetics/metabolism, Hydrogen Peroxide/metabolism, Kinetics, Molecular Sequence Data, Molecular Weight, Open Reading Frames/genetics, Oxidative Stress, Recombinant Proteins/chemistry/metabolism, Sequence Alignment, Sequence Homology, Amino Acid, Spectrophotometry, Ultraviolet10.1093/oxfordjournals.jbchem.a002865Metabolism
Enzymology11226881Purification and characterization of homo- and hetero-dimeric acetate kinases from the sulfate-reducing bacterium Desulfovibrio vulgaris.Yu L, Ishida T, Ozawa K, Akutsu H, Horiike KJ Biochem2001Acetate Kinase/chemistry/*isolation & purification/*metabolism, Adenosine Diphosphate/metabolism, Adenosine Triphosphate/metabolism, Amino Acid Sequence, Chromatography, High Pressure Liquid, Desulfovibrio vulgaris/*enzymology/metabolism, Dimerization, Enzyme Stability, Hydrogen-Ion Concentration, Kinetics, Lactic Acid/metabolism, Magnesium/pharmacology, Molecular Sequence Data, Molecular Weight, Protein Structure, Quaternary, Protein Subunits, Sulfates/metabolism10.1093/oxfordjournals.jbchem.a002872Metabolism
Metabolism12054869Redox-coupled conformational alternations in cytochrome c(3) from D. vulgaris Miyazaki F on the basis of its reduced solution structure.Harada E, Fukuoka Y, Ohmura T, Fukunishi A, Kawai G, Fujiwara T, Akutsu HJ Mol Biol2002Amino Acid Sequence, Binding Sites, Crystallography, X-Ray, Cytochrome c Group/*chemistry/*metabolism, Desulfovibrio vulgaris/*chemistry/*classification, Heme/chemistry/metabolism, Kinetics, Models, Molecular, Molecular Sequence Data, Nuclear Magnetic Resonance, Biomolecular, Oxidation-Reduction, Pliability, Protein Conformation, Solutions10.1016/S0022-2836(02)00367-4Enzymology
Metabolism12296727Structural studies of the carbon monoxide complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F: suggestion for the initial activation site for dihydrogen.Ogata H, Mizoguchi Y, Mizuno N, Miki K, Adachi S, Yasuoka N, Yagi T, Yamauchi O, Hirota S, Higuchi YJ Am Chem Soc2002Binding Sites, Carbon Monoxide/*chemistry/metabolism, Crystallography, X-Ray, Desulfovibrio vulgaris/*enzymology, Fourier Analysis, Hydrogen/*chemistry/metabolism, Hydrogenase/*chemistry/metabolism, Models, Molecular, Nickel/chemistry/metabolism, Protein Conformation, Spectrophotometry, Ultraviolet, Spectrum Analysis, Raman10.1021/ja012645kEnzymology
Metabolism12381206Pulsed electron-electron double resonance on multinuclear metal clusters: assignment of spin projection factors based on the dipolar interaction.Elsasser C, Brecht M, Bittl RJ Am Chem Soc2002Computer Simulation, Desulfovibrio vulgaris/enzymology, Electron Spin Resonance Spectroscopy, Fourier Analysis, Hydrogen/chemistry/metabolism, Hydrogenase/*chemistry/metabolism, Iron-Sulfur Proteins/*chemistry/metabolism, Models, Molecular10.1021/ja027348+Enzymology
Enzymology12515509Single crystal EPR studies of the reduced active site of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F.Foerster S, Stein M, Brecht M, Ogata H, Higuchi Y, Lubitz WJ Am Chem Soc2003Bacterial Proteins/chemistry/metabolism, Binding Sites, Desulfovibrio vulgaris/*enzymology, Electron Spin Resonance Spectroscopy, Hydrogenase/*chemistry/metabolism, Models, Chemical, Models, Molecular, Oxidation-Reduction, Protein Conformation10.1021/ja027522uMetabolism
Enzymology12761175Cloning and expression of the superoxide dismutase gene from the obligate anaerobic bacterium Desulfovibrio vulgaris (Miyazaki F).Nakanishi T, Inoue H, Kitamura MJ Biochem2003Amino Acid Sequence, Anaerobiosis/genetics, Bacterial Proteins/biosynthesis/chemistry/genetics/metabolism, Base Sequence, Cloning, Molecular/*methods, Desulfovibrio vulgaris/*enzymology/*genetics, Gene Expression Regulation, Enzymologic, *Genes, Bacterial, Superoxide Dismutase/*biosynthesis/chemistry/*genetics10.1093/jb/mvg051Metabolism
Enzymology14570480Direct detection of a hydrogen ligand in the [NiFe] center of the regulatory H2-sensing hydrogenase from Ralstonia eutropha in its reduced state by HYSCORE and ENDOR spectroscopy.Brecht M, van Gastel M, Buhrke T, Friedrich B, Lubitz WJ Am Chem Soc2003Computer Simulation, Cupriavidus necator/*enzymology, Electron Spin Resonance Spectroscopy/methods, Hydrogen/*chemistry, Hydrogen Bonding, Hydrogenase/*chemistry, Ligands, Models, Molecular, Oxidation-Reduction10.1021/ja036624x
Enzymology14581238Role of the aromatic ring of Tyr43 in tetraheme cytochrome c(3) from Desulfovibrio vulgaris Miyazaki F.Ozawa K, Takayama Y, Yasukawa F, Ohmura T, Cusanovich MA, Tomimoto Y, Ogata H, Higuchi Y, Akutsu HBiophys J2003Amino Acid Substitution, Computer Simulation, Cytochrome c Group/biosynthesis/*chemistry/genetics/*radiation effects, Desulfovibrio vulgaris/*chemistry/*enzymology, Enzyme Activation, Enzyme Stability, Heme/*chemistry, Hydrocarbons, Aromatic/chemistry, Lasers, *Models, Molecular, Mutagenesis, Site-Directed, Oxidation-Reduction, Photolysis, Protein Conformation, Recombinant Proteins, Structure-Activity Relationship, Tyrosine/*chemistry10.1016/S0006-3495(03)74756-0
Enzymology14746912Cloning and expression of the enolase gene from Desulfovibrio vulgaris (Miyazaki F).Kitamura M, Takayama Y, Kojima S, Kohno K, Ogata H, Higuchi Y, Inoue HBiochim Biophys Acta2004Amino Acid Sequence, Base Sequence, Cloning, Molecular, Desulfovibrio vulgaris/enzymology/*genetics/growth & development, Escherichia coli/metabolism, Glucose/metabolism, Glycerol/metabolism, Hydrogen-Ion Concentration, Kinetics, Lactic Acid/metabolism, Molecular Sequence Data, Molecular Weight, Phosphopyruvate Hydratase/biosynthesis/chemistry/*genetics, RNA, Messenger/analysis, Recombinant Proteins/chemistry, Reverse Transcriptase Polymerase Chain Reaction10.1016/j.bbaexp.2003.11.008Metabolism
14965285Crystallization and MAD data collection of high-molecular weight cytochrome c from Desulfovibrio vulgaris Miyazaki F.Shibata N, Suto K, Ichimura E, Yoshimura K, Muneo K, Tomigami S, Morimoto Y, Ogata M, Yagi T, Higuchi Y, Yasuoka NProtein Pept Lett2004Crystallization, Crystallography, X-Ray, Cytochromes c/*chemistry, Data Collection, Desulfovibrio vulgaris/*chemistry, Molecular Weight10.2174/0929866043478428
Enzymology15299378Location of active sites of NiFe hydrogenase determined by the combination of multiple isomorphous replacement and multiwavelength anomalous-diffraction methods.Higuchi Y, Okamoto T, Fujimoto K, Misaki SActa Crystallogr D Biol Crystallogr199410.1107/S0907444994002416
Genetics15323546Roles of noncoordinated aromatic residues in redox regulation of cytochrome c3 from Desulfovibrio vulgaris Miyazaki F.Takayama Y, Harada E, Kobayashi R, Ozawa K, Akutsu HBiochemistry2004Amino Acid Sequence, Amino Acid Substitution/genetics, Amino Acids, Aromatic/*chemistry/genetics, Cytochrome c Group/*chemistry/genetics, Desulfovibrio vulgaris/*enzymology/genetics, Electrochemistry, Heme/chemistry, Histidine/genetics, Leucine/genetics, Molecular Sequence Data, Mutagenesis, Site-Directed, Nuclear Magnetic Resonance, Biomolecular, Oxidation-Reduction, Phenylalanine/chemistry/genetics, Tyrosine/chemistry/genetics10.1021/bi049551iEnzymology
Enzymology15611882An orientation-selected ENDOR and HYSCORE study of the Ni-C active state of Desulfovibrio vulgaris Miyazaki F hydrogenase.Foerster S, van Gastel M, Brecht M, Lubitz WJ Biol Inorg Chem2004Binding Sites, Carbon/chemistry/*metabolism, Desulfovibrio vulgaris/*enzymology, Electron Spin Resonance Spectroscopy, Hydrogenase/*chemistry/*metabolism, Nickel/chemistry/*metabolism, Spectrum Analysis10.1007/s00775-004-0613-5Metabolism
Enzymology15667250EPR experiments to elucidate the structure of the ready and unready states of the [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F.van Gastel M, Fichtner C, Neese F, Lubitz WBiochem Soc Trans2005Desulfovibrio vulgaris/*enzymology, Electron Spin Resonance Spectroscopy, Hydrogenase/*chemistry, Protein Conformation, Spectroscopy, Fourier Transform Infrared10.1042/BST0330007
Enzymology16292669A single-crystal ENDOR and density functional theory study of the oxidized states of the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F.van Gastel M, Stein M, Brecht M, Schroder O, Lendzian F, Bittl R, Ogata H, Higuchi Y, Lubitz WJ Biol Inorg Chem2005Binding Sites, Crystallization, Cysteine/chemistry, Desulfovibrio vulgaris/*enzymology, Electron Spin Resonance Spectroscopy/methods, Hydrogenase/*chemistry/metabolism, Ligands, Oxidation-Reduction, Protein Conformation, Protons, Sulfur/chemistry10.1007/s00775-005-0048-7Metabolism
Enzymology16460012Redox interaction of cytochrome c3 with [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F.Yahata N, Saitoh T, Takayama Y, Ozawa K, Ogata H, Higuchi Y, Akutsu HBiochemistry2006Binding Sites, Cytochrome c Group/chemistry/*metabolism, Desulfovibrio vulgaris/*enzymology, Heme/metabolism, Hydrogenase/*metabolism, Kinetics, Magnetic Resonance Spectroscopy/methods, Methionine/chemistry/metabolism, Models, Molecular, Oxidation-Reduction10.1021/bi0514360Metabolism
Enzymology16610917Hydrogen bonding affects the [NiFe] active site of Desulfovibrio vulgaris Miyazaki F hydrogenase: a hyperfine sublevel correlation spectroscopy and density functional theory study.Agrawal AG, van Gastel M, Gartner W, Lubitz WJ Phys Chem B2006Chemical Phenomena, Chemistry, Physical, Cysteine/chemistry, Desulfovibrio vulgaris/*enzymology, Electron Spin Resonance Spectroscopy, Histidine/chemistry, Hydrogen Bonding, Hydrogenase/*chemistry, Models, Molecular10.1021/jp0573902
16887609Membrane-bound cytochromes in a sulfate-reducing strict anaerobe Desulfovibrio vulgaris Miyazaki F.Ozawa K, Mogi T, Suzuki M, Kitamura M, Nakaya T, Anraku Y, Akutsu HAnaerobe199710.1006/anae.1997.0114
Enzymology16893172Spectroelectrochemical characterization of the [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F.Fichtner C, Laurich C, Bothe E, Lubitz WBiochemistry2006Crystallography, X-Ray, Desulfovibrio vulgaris/*classification/*enzymology, Electrochemistry, Hydrogen-Ion Concentration, Hydrogenase/*chemistry, Oxidation-Reduction, Spectroscopy, Fourier Transform Infrared, Vibration10.1021/bi0602462Phylogeny
Metabolism16902753Sequential and structural analysis of [NiFe]-hydrogenase-maturation proteins from Desulfovibrio vulgaris Miyazaki F.Agrawal AG, Voordouw G, Gartner WAntonie Van Leeuwenhoek2006Amino Acid Sequence, Bacterial Proteins/*chemistry/*metabolism, Desulfovibrio vulgaris/*genetics/*metabolism, Gene Expression Regulation, Bacterial, Gene Expression Regulation, Enzymologic, Hydrogenase/*metabolism, Molecular Sequence Data, Phylogeny10.1007/s10482-006-9082-xEnzymology
Metabolism17150519Application of cell-free translation systems to studies of cofactor binding proteins.Abe M, Hori H, Nakanishi T, Arisaka F, Ogasawara T, Sawasaki T, Kitamura M, Endo YNucleic Acids Symp Ser (Oxf)2004Bacterial Proteins/biosynthesis/*metabolism, Cell-Free System, Desulfovibrio vulgaris/*metabolism, Flavin Mononucleotide/*metabolism, Protein Binding, *Protein Biosynthesis, Time Factors10.1093/nass/48.1.143
Enzymology17507210Superoxide radical sensing using a cytochrome c3 immobilized conducting polymer electrode.Darain F, Park JS, Akutsu H, Shim YBBiosens Bioelectron2007Biosensing Techniques/*instrumentation, Cytochrome c Group/*chemistry, Electric Conductivity, Enzymes, Immobilized/chemistry, Equipment Design, Equipment Failure Analysis, *Microelectrodes, Polymers/*chemistry, Reproducibility of Results, Sensitivity and Specificity, Superoxides/*analysis10.1016/j.bios.2007.03.026
Phylogeny18607091Crystallization and preliminary X-ray analysis of a class II release factor RF3 from a sulfate-reducing bacterium.Kihira K, Numata S, Kitamura M, Kondo J, Terawaki S, Shomura Y, Komori H, Shibata N, Higuchi YActa Crystallogr Sect F Struct Biol Cryst Commun2008Bacterial Proteins/*chemistry/*classification/genetics, Crystallization, Desulfovibrio vulgaris/*chemistry/genetics, Gene Expression Regulation, Bacterial, Peptide Termination Factors/*chemistry/*classification/genetics, Sulfates/*chemistry/metabolism, X-Ray Diffraction10.1107/S1744309108015583Metabolism
Metabolism18702516Strategic roles of axial histidines in structure formation and redox regulation of tetraheme cytochrome c3.Takayama Y, Werbeck ND, Komori H, Morita K, Ozawa K, Higuchi Y, Akutsu HBiochemistry2008Amino Acid Substitution, Bacterial Proteins/*chemistry/metabolism, Crystallography, X-Ray, Cytochrome c Group/*chemistry/genetics, Desulfovibrio vulgaris/*enzymology/genetics, Histidine/chemistry/genetics, Hydrogen Bonding, Ligands, Mutation, Missense, Nuclear Magnetic Resonance, Biomolecular, Oxidation-Reduction, Protein Structure, Tertiary/physiology10.1021/bi8005708Enzymology
Enzymology18765921Crystallization and preliminary X-ray crystallographic study of flavoredoxin from Desulfovibrio vulgaris Miyazaki F.Ueda Y, Shibata N, Takeuchi D, Kitamura M, Higuchi YActa Crystallogr Sect F Struct Biol Cryst Commun2008Crystallization, Crystallography, X-Ray, Desulfovibrio vulgaris/*chemistry, Flavoproteins/*chemistry/isolation & purification, Oxidoreductases/*chemistry/isolation & purification, Protein Structure, Tertiary10.1107/S1744309108025840Phylogeny
18800855Simultaneous analysis of ultrafast fluorescence decays of FMN binding protein and its mutated proteins by molecular dynamic simulation and electron transfer theory.Nunthaboot N, Tanaka F, Kokpol S, Chosrowjan H, Taniguchi S, Mataga NJ Phys Chem B2008Algorithms, Amino Acid Substitution, Bacterial Proteins/*chemistry/genetics, Computer Simulation, Desulfovibrio vulgaris, Electron Transport/*physiology, Flavin Mononucleotide/*chemistry, Flavoproteins/*chemistry/genetics, Fluorescence, Models, Chemical, Protein Structure, Tertiary, Thermodynamics, Time Factors10.1021/jp804130j
Enzymology18997328Purification, crystallization and preliminary X-ray analysis of adenylylsulfate reductase from Desulfovibrio vulgaris Miyazaki F.Ogata H, Goenka Agrawal A, Kaur AP, Goddard R, Gartner W, Lubitz WActa Crystallogr Sect F Struct Biol Cryst Commun2008Bacterial Proteins/*chemistry/genetics/*isolation & purification, Crystallization/methods, Desulfovibrio vulgaris/*enzymology, Molecular Sequence Data, Oxidoreductases Acting on Sulfur Group Donors/*chemistry/genetics/*isolation & purification, X-Ray Diffraction10.1107/S1744309108029588Phylogeny
Enzymology19151100Cloning and expression of the MutM gene from obligate anaerobic bacterium Desulfovibrio vulgaris (Miyazaki F).Sanada H, Nakanishi T, Inoue H, Kitamura MJ Biochem2009Anaerobiosis, Bacterial Proteins/chemistry/*genetics/metabolism, Base Sequence, Cloning, Molecular, DNA, Bacterial/metabolism, Desulfovibrio vulgaris/*enzymology/*genetics, Gene Expression Regulation, Bacterial, Genome, Bacterial/genetics, Immunoblotting, Kinetics, Metals/metabolism, Molecular Sequence Data, Molecular Weight, Recombinant Proteins/metabolism, Reverse Transcriptase Polymerase Chain Reaction, Sequence Alignment, Spectrophotometry, Atomic10.1093/jb/mvp005Metabolism
Metabolism19626348Probing intermediates in the activation cycle of [NiFe] hydrogenase by infrared spectroscopy: the Ni-SIr state and its light sensitivity.Pandelia ME, Ogata H, Currell LJ, Flores M, Lubitz WJ Biol Inorg Chem2009Bacterial Proteins/chemistry/*metabolism, Carbon Monoxide/metabolism, Desulfovibrio vulgaris/*enzymology, Enzyme Activation, Hydrogen Bonding, Hydrogenase/chemistry/*metabolism, Isotopes/metabolism, *Light, Models, Molecular, Nickel/*metabolism, Oxidation-Reduction, Protein Conformation, Spectrophotometry, Infrared, Spectroscopy, Fourier Transform Infrared10.1007/s00775-009-0566-9Enzymology
Metabolism19708087Structure analysis of the flavoredoxin from Desulfovibrio vulgaris Miyazaki F reveals key residues that discriminate the functions and properties of the flavin reductase family.Shibata N, Ueda Y, Takeuchi D, Haruyama Y, Kojima S, Sato J, Niimura Y, Kitamura M, Higuchi YFEBS J2009Amino Acid Sequence, Binding Sites, Cloning, Molecular, Crystallography, X-Ray, Cysteine/chemistry/metabolism, Desulfovibrio vulgaris/*metabolism, Escherichia coli/metabolism, FMN Reductase/chemistry/metabolism, Flavin Mononucleotide/metabolism, Flavoproteins/*chemistry/metabolism, *Models, Molecular, Molecular Sequence Data, Oxidoreductases/*chemistry/metabolism, Protein Conformation, Recombinant Proteins/chemistry/metabolism10.1111/j.1742-4658.2009.07184.xEnzymology
Enzymology19759926[NiFe] hydrogenases: structural and spectroscopic studies of the reaction mechanism.Ogata H, Lubitz W, Higuchi YDalton Trans2009Biocatalysis, Carbon Monoxide/pharmacology, Enzyme Inhibitors/pharmacology, Hydrogenase/antagonists & inhibitors/*chemistry/*metabolism, Oxidation-Reduction, Spectrum Analysis10.1039/b903840jMetabolism
Enzymology19845323Spectroelectrochemical study of the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F in solution and immobilized on biocompatible gold surfaces.Millo D, Pandelia ME, Utesch T, Wisitruangsakul N, Mroginski MA, Lubitz W, Hildebrandt P, Zebger IJ Phys Chem B2009Argon/chemistry, Catalytic Domain, Desulfovibrio vulgaris/*enzymology, *Electrochemical Techniques, Electrodes, Enzymes, Immobilized/chemistry/metabolism, Gold/*chemistry, Hydrogen/chemistry, Hydrogenase/*chemistry/metabolism, Oxidation-Reduction, *Spectrophotometry, Infrared10.1021/jp906575rMetabolism
Enzymology19925776Inhibition of the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F by carbon monoxide: an FTIR and EPR spectroscopic study.Pandelia ME, Ogata H, Currell LJ, Flores M, Lubitz WBiochim Biophys Acta2009Antimetabolites/*pharmacology, Carbon Monoxide/*pharmacology, Desulfovibrio vulgaris/*enzymology, *Electron Spin Resonance Spectroscopy, Hydrogenase/*antagonists & inhibitors/chemistry/metabolism, Kinetics, Light, Models, Chemical, Nickel/chemistry/metabolism, *Spectroscopy, Fourier Transform Infrared10.1016/j.bbabio.2009.11.002Metabolism
Enzymology20165762Comparison of the membrane-bound [NiFe] hydrogenases from R. eutropha H16 and D. vulgaris Miyazaki F in the oxidized ready state by pulsed EPR.Saggu M, Teutloff C, Ludwig M, Brecht M, Pandelia ME, Lenz O, Friedrich B, Lubitz W, Hildebrandt P, Lendzian F, Bittl RPhys Chem Chem Phys2010Catalytic Domain, Cupriavidus necator/*enzymology, Desulfovibrio vulgaris/*enzymology, Electron Spin Resonance Spectroscopy, Hydrogen Bonding, Hydrogenase/*chemistry, Oxidation-Reduction, Spin Labels10.1039/b922236g
Enzymology20221530Concerto catalysis--harmonising [NiFe]hydrogenase and NiRu model catalysts.Ichikawa K, Nonaka K, Matsumoto T, Kure B, Yoon KS, Higuchi Y, Yagi T, Ogo SDalton Trans2010Bacterial Proteins/chemistry/*metabolism, *Catalysis, Desulfovibrio vulgaris/enzymology, Hydrogen/chemistry, Hydrogen-Ion Concentration, Hydrogenase/chemistry/*metabolism, Models, Molecular, Protein Conformation, Ruthenium/*chemistry10.1039/b926061gMetabolism
Enzymology20301175Intermediates in the catalytic cycle of [NiFe] hydrogenase: functional spectroscopy of the active site.Pandelia ME, Ogata H, Lubitz WChemphyschem2010Biocatalysis, Catalytic Domain, Electron Spin Resonance Spectroscopy, Hydrogenase/*chemistry/metabolism, Oxidation-Reduction, Protein Structure, Tertiary, Spectroscopy, Fourier Transform Infrared10.1002/cphc.200900950Metabolism
20397678Effects of the disappearance of one charge on ultrafast fluorescence dynamics of the FMN binding protein.Chosrowjan H, Taniguchi S, Mataga N, Nakanishi T, Haruyama Y, Sato S, Kitamura M, Tanaka FJ Phys Chem B2010Carrier Proteins, Crystallography, X-Ray, Flavin Mononucleotide/*chemistry, Fluorescence, Hydrogen Bonding, X-Ray Diffraction10.1021/jp912137s
Enzymology20449009FTIR study on the light sensitivity of the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F: Ni-C to Ni-L photoconversion, kinetics of proton rebinding and H/D isotope effect.Kellers P, Pandelia ME, Currell LJ, Gorner H, Lubitz WPhys Chem Chem Phys2009Catalytic Domain, Desulfovibrio vulgaris/*enzymology, Deuterium/*chemistry, Hydrogen/*chemistry, Hydrogenase/*chemistry/metabolism, Kinetics, *Light, Models, Molecular, Photochemistry, *Protons, Spectroscopy, Fourier Transform Infrared, Temperature, Water/chemistry10.1039/b913635eMetabolism
Enzymology21045297Purification, crystallization and preliminary X-ray analysis of the dissimilatory sulfite reductase from Desulfovibrio vulgaris Miyazaki F.Ogata H, Shomura Y, Goenka Agrawal A, Kaur AP, Gartner W, Higuchi Y, Lubitz WActa Crystallogr Sect F Struct Biol Cryst Commun2010Crystallization, Crystallography, X-Ray, Desulfovibrio vulgaris/*enzymology, Hydrogensulfite Reductase/*chemistry/isolation & purification, Models, Molecular, Protein Structure, Tertiary10.1107/S1744309110033191Phylogeny
21347481Simultaneous analyses of photoinduced electron transfer in the wild type and four single substitution isomers of the FMN binding protein from Desulfovibrio vulgaris, Miyazaki F.Nunthaboot N, Pianwanit S, Kokpol S, Tanaka FPhys Chem Chem Phys2011Amino Acid Substitution, Bacterial Proteins/*chemistry, Flavoproteins/*chemistry, Isomerism, Models, Molecular, Molecular Dynamics Simulation, Photochemistry10.1039/c0cp02634d
Enzymology23053531Computational study of the electronic structure and magnetic properties of the Ni-C state in [NiFe] hydrogenases including the second coordination sphere.Kampa M, Lubitz W, van Gastel M, Neese FJ Biol Inorg Chem2012Carbon/*chemistry, Coordination Complexes/*chemistry, *Electrons, Hydrogenase/*chemistry, Magnetics, Models, Molecular, Nickel/*chemistry, *Quantum Theory10.1007/s00775-012-0941-9
Enzymology23159801Photosensitivity of the Ni-A state of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F with visible light.Osuka H, Shomura Y, Komori H, Shibata N, Nagao S, Higuchi Y, Hirota SBiochem Biophys Res Commun2012Desulfovibrio vulgaris/*enzymology, Hydrogenase/chemistry/*radiation effects, Iron/chemistry, *Light, Nickel/chemistry, *Photochemical Processes, Spectroscopy, Fourier Transform Infrared10.1016/j.bbrc.2012.10.136
Enzymology23201506Novel H2-oxidizing [NiFeSe]hydrogenase from Desulfovibrio vulgaris Miyazaki F.Nonaka K, Nguyen NT, Yoon KS, Ogo SJ Biosci Bioeng2012Amino Acid Sequence, Biocatalysis, Desulfovibrio vulgaris/*enzymology/genetics, Hydrogenase/chemistry/genetics/*metabolism, Molecular Sequence Data, Oxidation-Reduction, Sequence Alignment10.1016/j.jbiosc.2012.10.011Genetics
Enzymology23215250Effect of the protonation degree of a self-assembled monolayer on the immobilization dynamics of a [NiFe] hydrogenase.Utesch T, Millo D, Castro MA, Hildebrandt P, Zebger I, Mroginski MALangmuir2013Adsorption, Alkanes/chemistry, Bacterial Proteins/*chemistry, Desulfovibrio gigas/*chemistry/enzymology, Desulfovibrio vulgaris/*chemistry/enzymology, Electrodes, Gold/chemistry, Hydrogen-Ion Concentration, Hydrogenase/*chemistry, Immobilized Proteins/*chemistry, Kinetics, Molecular Dynamics Simulation, *Protons, Sulfhydryl Compounds/chemistry, Thermodynamics10.1021/la303635q
Enzymology24038675Spectroscopic and electrochemical characterization of the [NiFeSe] hydrogenase from Desulfovibrio vulgaris Miyazaki F: reversible redox behavior and interactions between electron transfer centers.Riethausen J, Rudiger O, Gartner W, Lubitz W, Shafaat HSChembiochem2013Desulfovibrio vulgaris/*enzymology, Electrochemical Techniques, Electron Spin Resonance Spectroscopy, Electron Transport, Electrons, Hydrogenase/*chemistry/metabolism, Oxidation-Reduction, Spectroscopy, Fourier Transform Infrared, Temperature10.1002/cbic.201300120Metabolism
24108633Photoinduced electron transfer modeling to simulate flavoprotein fluorescence decay.Nunthaboot N, Lugsanangarm K, Nueangaudom A, Pianwanit S, Kokpol S, Tanaka FMethods Mol Biol2014Carrier Proteins/chemistry, Desulfovibrio vulgaris/chemistry, Electron-Transferring Flavoproteins/*chemistry, Flavin Mononucleotide/chemistry, *Fluorescence, Molecular Dynamics Simulation, Photochemistry/methods, Solutions/chemistry, Tryptophan/*chemistry, Tyrosine/chemistry10.1007/978-1-62703-649-8_14
Metabolism25773195Surface display of highly-stable Desulfovibrio vulgaris carbonic anhydrase on polyester beads for CO2 capture.Hooks DO, Rehm BHBiotechnol Lett2015Bacterial Proteins/chemistry/genetics/*metabolism, Carbon Dioxide/metabolism, Carbonic Anhydrases/chemistry/genetics/*metabolism, Cell Surface Display Techniques, Desulfovibrio vulgaris/*enzymology/genetics, Enzymes, Immobilized/chemistry/genetics/*metabolism, Escherichia coli/genetics/metabolism, Polyesters/*chemistry, Recombinant Proteins/chemistry/genetics/*metabolism10.1007/s10529-015-1803-7Enzymology
Enzymology25898020FT-IR Characterization of the Light-Induced Ni-L2 and Ni-L3 States of [NiFe] Hydrogenase from Desulfovibrio vulgaris Miyazaki F.Tai H, Nishikawa K, Inoue S, Higuchi Y, Hirota SJ Phys Chem B2015Desulfovibrio vulgaris/*enzymology, Electron Spin Resonance Spectroscopy, Hydrogenase/*chemistry/metabolism, *Light, Nickel/*chemistry/metabolism, Organometallic Compounds/*chemistry/metabolism, Spectroscopy, Fourier Transform Infrared, Thermodynamics10.1021/acs.jpcb.5b03075Metabolism
Enzymology26259066Hydride bridge in [NiFe]-hydrogenase observed by nuclear resonance vibrational spectroscopy.Ogata H, Kramer T, Wang H, Schilter D, Pelmenschikov V, van Gastel M, Neese F, Rauchfuss TB, Gee LB, Scott AD, Yoda Y, Tanaka Y, Lubitz W, Cramer SPNat Commun2015Desulfovibrio vulgaris/*enzymology, Hydrogenase/*chemistry, Magnetic Resonance Spectroscopy10.1038/ncomms8890
Enzymology26277806Light-Driven Hydrogen Production by Hydrogenases and a Ru-Complex inside a Nanoporous Glass Plate under Aerobic External Conditions.Noji T, Kondo M, Jin T, Yazawa T, Osuka H, Higuchi Y, Nango M, Itoh S, Dewa TJ Phys Chem Lett201410.1021/jz5008164Biotechnology
Enzymology27456760Photoactivation of the Ni-SIr state to the Ni-SIa state in [NiFe] hydrogenase: FT-IR study on the light reactivity of the ready Ni-SIr state and as-isolated enzyme revisited.Tai H, Xu L, Inoue S, Nishikawa K, Higuchi Y, Hirota SPhys Chem Chem Phys2016Desulfovibrio vulgaris/*enzymology, Hydrogenase/*metabolism, Light, Photochemistry10.1039/c6cp04628bPhylogeny
27857559Roles of charged residues in pH-dependent redox properties of cytochrome c3 from Desulfovibrio vulgaris Miyazaki F.Yahata N, Ozawa K, Tomimoto Y, Morita K, Komori H, Ogata H, Higuchi Y, Akutsu HBiophysics (Nagoya-shi)200610.2142/biophysics.2.45
Enzymology28192203Electrostatic roles in electron transfer from [NiFe] hydrogenase to cytochrome c3 from Desulfovibrio vulgaris Miyazaki F.Sugimoto Y, Kitazumi Y, Shirai O, Nishikawa K, Higuchi Y, Yamamoto M, Kano KBiochim Biophys Acta Proteins Proteom2017Cell Respiration, Cytochrome c Group/*chemistry/metabolism, Desulfovibrio vulgaris/*enzymology, Electron Transport, Electrons, Hydrogenase/*chemistry/metabolism, Kinetics, *Models, Molecular, Osmolar Concentration, Oxidation-Reduction, *Protein Conformation, Protein Interaction Maps, Static Electricity10.1016/j.bbapap.2017.02.009Metabolism
Enzymology29753939Reactivation of standard [NiFe]-hydrogenase and bioelectrochemical catalysis of proton reduction and hydrogen oxidation in a mediated-electron-transfer system.Shiraiwa S, So K, Sugimoto Y, Kitazumi Y, Shirai O, Nishikawa K, Higuchi Y, Kano KBioelectrochemistry2018Biocatalysis, Biosensing Techniques, Desulfovibrio vulgaris/chemistry/*enzymology/metabolism, Electron Transport, Enzyme Activation, Enzymes, Immobilized/chemistry/*metabolism, Hydrogen/*metabolism, Hydrogenase/chemistry/*metabolism, Models, Molecular, Oxidation-Reduction, Protons, Thermodynamics, Viologens/chemistry10.1016/j.bioelechem.2018.05.003Metabolism
Enzymology30609080New assay method based on Raman spectroscopy for enzymes reacting with gaseous substrates.Kawahara-Nakagawa Y, Nishikawa K, Nakashima S, Inoue S, Ohta T, Ogura T, Shigeta Y, Fukutani K, Yagi T, Higuchi YProtein Sci2019Catalysis, Catalytic Domain, Desulfovibrio vulgaris/*enzymology, Enzyme Assays/*methods, Gases/chemistry/metabolism, Hydrogen/*chemistry/metabolism, Hydrogenase/chemistry/*metabolism, Spectrum Analysis, Raman/*methods10.1002/pro.3569Metabolism
Enzymology31354654H2 Kinetic Isotope Fractionation Superimposed by Equilibrium Isotope Fractionation During Hydrogenase Activity of D. vulgaris Strain Miyazaki.Loffler M, Kummel S, Vogt C, Richnow HHFront Microbiol201910.3389/fmicb.2019.01545
Enzymology33021496Towards cryogenic neutron crystallography on the reduced form of [NiFe]-hydrogenase.Hiromoto T, Nishikawa K, Inoue S, Matsuura H, Hirano Y, Kurihara K, Kusaka K, Cuneo M, Coates L, Tamada T, Higuchi YActa Crystallogr D Struct Biol2020Crystallography/*methods, Desulfovibrio vulgaris/enzymology, Freezing, Hydrogenase/*chemistry, Models, Molecular, Neutron Diffraction/*methods10.1107/S2059798320011365

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8227Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19637)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19637
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67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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