Strain identifier
BacDive ID: 4163
Type strain:
Species: Nitratidesulfovibrio vulgaris
Strain Designation: Miyazaki F
Strain history: H. Akutsu <-- S. Iwasaki strain Miyazaki F.
NCBI tax ID(s): 881 (species)
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
@ref | history |
---|---|
8227 | <- J.D. Wall <- H. Akutso, Yokohama National University <- Osaka University <- Tokyo University <- Ajinomoto Co. Inc.; Miyazaki F {1949} |
67770 | H. 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
8227 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 8227
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
8227 | degraded paddy field | Miyazaki | Japan | JPN | Asia |
67770 | Paddy field soil in Miyazaki | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
topic | Pubmed-ID | title | authors | journal | year | mesh | DOI | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 479126 | Crystallographic data for cytochrome c3 from two strains of Desulfovibrio vulgaris, Miyazaki. | Bando S, Matsuura Y, Tanaka N, Yasuoka N, Kakudo M, Yagi T, Inokuchi H | J Biochem | 1979 | *Cytochromes, Desulfovibrio/*analysis, Protein Conformation, Species Specificity, X-Ray Diffraction | ||
Enzymology | 1332780 | Reduction kinetics of the four hemes of cytochrome c3 from Desulfovibrio vulgaris by flash photolysis. | Akutsu H, Hazzard JH, Bartsch RG, Cusanovich MA | Biochim Biophys Acta | 1992 | Cytochrome c Group/*chemistry/isolation & purification, Desulfovibrio vulgaris/*enzymology, Edetic Acid, Heme/chemistry, Hydrogen-Ion Concentration, Kinetics, Oxidation-Reduction | 10.1016/0005-2728(92)90003-k | Phylogeny |
1333991 | Assignment 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 AV | FEBS Lett | 1992 | Cytochrome c Group/*chemistry, Desulfovibrio vulgaris/*chemistry, Heme/*chemistry, Magnetic Resonance Spectroscopy/methods, Oxidation-Reduction, Structure-Activity Relationship, X-Ray Diffraction | 10.1016/0014-5793(92)80963-h | ||
Metabolism | 1336461 | Structural studies of Desulfovibrio vulgaris ferrocytochrome c3 by two-dimensional NMR. | Turner DL, Salgueiro CA, LeGall J, Xavier AV | Eur J Biochem | 1992 | Amino Acid Sequence, Cytochrome c Group/*chemistry, Desulfovibrio vulgaris/*metabolism, Heme/analysis, Magnetic Resonance Spectroscopy/methods, Models, Molecular, Protein Conformation | 10.1111/j.1432-1033.1992.tb17497.x | |
Metabolism | 1668723 | 1H 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 H | J Biomol NMR | 1991 | Binding 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 Conformation | 10.1007/BF01875520 | Enzymology |
Phylogeny | 1964450 | S-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 T | J Biochem | 1990 | Amino Acid Sequence, Cytochrome c Group/*chemistry/classification/genetics, Desulfovibrio/*enzymology/genetics, Molecular Sequence Data, Phylogeny, Protein Conformation, X-Ray Diffraction | 10.1093/oxfordjournals.jbchem.a123267 | Genetics |
Enzymology | 2081730 | Redox 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 H | J Biochem | 1990 | Binding Sites, Cluster Analysis, Desulfovibrio/*enzymology, Iron/chemistry/*metabolism, Oxidation-Reduction, Oxidoreductases/chemistry/*metabolism, Solubility, Spectrum Analysis, Raman, Sulfur/chemistry/*metabolism | 10.1093/oxfordjournals.jbchem.a123269 | Metabolism |
Metabolism | 2159795 | Estimation 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 K | Biochemistry | 1990 | Cytochrome c Group/*metabolism, Desulfovibrio/*enzymology, *Heme, Magnetic Resonance Spectroscopy, Oxidation-Reduction | 10.1021/bi00461a008 | Enzymology |
Enzymology | 2269874 | Cloning and sequencing of a [NiFe] hydrogenase operon from Desulfovibrio vulgaris Miyazaki F. | Deckers HM, Wilson FR, Voordouw G | J Gen Microbiol | 1990 | Amino 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 Acid | 10.1099/00221287-136-10-2021 | Genetics |
Enzymology | 2987196 | Analysis of the active center of hydrogenase from Desulfovibrio vulgaris Miyazaki by magnetic measurements. | Yagi T, Kimura K, Inokuchi H | J Biochem | 1985 | Desulfovibrio/*enzymology, Electron Spin Resonance Spectroscopy, Ferricyanides/pharmacology, Hydrogenase/*analysis, Iron/analysis, Microwaves, Nickel/analysis, Spectrometry, Gamma, Temperature, Zinc/analysis | 10.1093/oxfordjournals.jbchem.a135042 | |
Enzymology | 2993256 | Purification and properties of thiosulfate reductase from Desulfovibrio vulgaris, Miyazaki F. | Aketagawa J, Kobayashi K, Ishimoto M | J Biochem | 1985 | Cytochrome 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, Sulfurtransferases | 10.1093/oxfordjournals.jbchem.a135144 | Metabolism |
Metabolism | 3023304 | Pyruvate dehydrogenase and the path of lactate degradation in Desulfovibrio vulgaris Miyazaki F. | Ogata M, Yagi T | J Biochem | 1986 | Acetyl 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, Temperature | 10.1093/oxfordjournals.jbchem.a121717 | Enzymology |
Enzymology | 3546297 | Single crystals of hydrogenase from Desulfovibrio vulgaris Miyazaki F. | Higuchi Y, Yasuoka N, Kakudo M, Katsube Y, Yagi T, Inokuchi H | J Biol Chem | 1987 | Chromatography, High Pressure Liquid, Crystallization, Desulfovibrio/*enzymology, Diffusion, Glycols, *Hydrogenase, Polyethylene Glycols | S0021-9258(18)61580-7 | |
Enzymology | 3897216 | Magnetic susceptibility of hydrogenase from Desulfovibrio vulgaris. | Kimura K, Inokuchi H, Nanami H, Yagi T | J Biochem | 1985 | Desulfovibrio/*enzymology, Hydrogenase/*analysis, Iron-Sulfur Proteins/analysis, Magnetics, Models, Chemical, Temperature | 10.1093/oxfordjournals.jbchem.a135246 | |
Enzymology | 6874662 | Characterization of periplasmic hydrogenase from Desulfovibrio vulgaris Miyazaki K. | Aketagawa J, Kobayashi K, Ishimoto M | J Biochem | 1983 | Amino Acids/analysis, Chemical Phenomena, Chemistry, Desulfovibrio/*enzymology, Immunochemistry, Molecular Weight, Oxidoreductases/*isolation & purification | 10.1093/jb/93.3.755 | Phylogeny |
Enzymology | 7548038 | Structure 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 MA | Biochemistry | 1995 | Crystallography, X-Ray, Cytochrome c Group/*chemistry, Desulfovibrio/*enzymology, Electron Spin Resonance Spectroscopy, Hydrogen Bonding, Models, Molecular, Oxidation-Reduction, Protein Conformation | 10.1021/bi00039a044 | |
Enzymology | 7783682 | A 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 T | Microbiol Immunol | 1995 | Amino 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 Acid | 10.1111/j.1348-0421.1995.tb02172.x | Genetics |
Enzymology | 8119891 | Novel 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 I | J Biol Chem | 1994 | Amino 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-Reduction | S0021-9258(17)37499-9 | Metabolism |
Metabolism | 8254667 | Structure analysis of cytochrome c3 from Desulfovibrio vulgaris Hildenborough at 1.9 A resolution. | Matias PM, Frazao C, Morais J, Coll M, Carrondo MA | J Mol Biol | 1993 | Amino 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/methods | 10.1006/jmbi.1993.1620 | Genetics |
Enzymology | 9116039 | Cloning 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 T | Biochim Biophys Acta | 1997 | Amino 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/analysis | 10.1016/s0167-4781(96)00203-5 | Genetics |
Enzymology | 9562622 | Cloning 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 T | J Biochem | 1998 | Base 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, Ultraviolet | 10.1093/oxfordjournals.jbchem.a022021 | Metabolism |
Metabolism | 9726950 | Ionic strength-dependent physicochemical factors in cytochrome c3 regulating the electron transfer rate. | Ohmura T, Nakamura H, Niki K, Cusanovich MA, Akutsu H | Biophys J | 1998 | Biophysical 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 Electricity | 10.1016/S0006-3495(98)74067-6 | Enzymology |
Genetics | 10089348 | Structure determination of rubredoxin from Desulfovibrio vulgaris Miyazaki F in two crystal forms. | Misaki S, Morimoto Y, Ogata M, Yagi T, Higuchi Y, Yasuoka N | Acta Crystallogr D Biol Crystallogr | 1999 | Amino Acid Sequence, Crystallography, X-Ray, Desulfovibrio vulgaris/*chemistry, Iron/chemistry, Models, Molecular, Molecular Sequence Data, Protein Conformation, Rubredoxins/*chemistry, Sequence Homology, Amino Acid | 10.1107/s0907444998011810 | |
Metabolism | 10216314 | Crystallization 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 N | Acta Crystallogr D Biol Crystallogr | 1999 | Bacterial Proteins/*chemistry, Carrier Proteins/*chemistry, Crystallization, Crystallography, X-Ray, Desulfovibrio vulgaris/*chemistry, Flavin Mononucleotide/*metabolism, *Flavoproteins, Protein Conformation | 10.1107/s0907444999003169 | |
Metabolism | 10378274 | Removal 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 T | Structure | 1999 | Binding Sites, Crystallography, X-Ray, Hydrogen/*chemistry, Hydrogenase/*chemistry/metabolism, Iron/*metabolism, Ligands, Models, Molecular, Nickel/*metabolism, Protein Conformation | 10.1016/s0969-2126(99)80071-9 | Enzymology |
10713530 | How 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 N | Acta Crystallogr D Biol Crystallogr | 2000 | Bacterial Proteins/*chemistry, Carrier Proteins/*chemistry, Crystallization, Crystallography, X-Ray, Desulfovibrio vulgaris/*chemistry, Dimerization, *Flavoproteins, Magnetic Resonance Spectroscopy, Models, Molecular, Protein Conformation, Solvents, Xylenes | 10.1107/s0907444900000111 | ||
Enzymology | 10735863 | Evidence 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 H | J Bacteriol | 2000 | Amino 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/*metabolism | 10.1128/JB.182.8.2200-2206.2000 | Genetics |
Enzymology | 10766434 | Single 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 W | J Biol Inorg Chem | 2000 | Binding Sites, Desulfovibrio vulgaris/*enzymology, Electron Spin Resonance Spectroscopy/*methods, Hydrogenase/*chemistry/metabolism, Models, Molecular, Protein Conformation | 10.1007/pl00010654 | Metabolism |
Metabolism | 10966450 | Expression 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 H | Appl Environ Microbiol | 2000 | Aerobiosis, Anaerobiosis, Cytochrome c Group/chemistry/*genetics/*metabolism, Desulfovibrio vulgaris/genetics/*metabolism, Plasmids/genetics, Recombinant Proteins/chemistry/metabolism, Shewanella/*genetics/growth & development/metabolism | 10.1128/AEM.66.9.4168-4171.2000 | |
Enzymology | 11001090 | The presence of a SO molecule in [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki as detected by mass spectrometry. | Higuchi Y, Toujou F, Tsukamoto K, Yagi T | J Inorg Biochem | 2000 | Desulfovibrio vulgaris/chemistry/*enzymology, Hydrogenase/*chemistry/isolation & purification, Mass Spectrometry/*methods, Molecular Structure, Protein Denaturation, Spectroscopy, Fourier Transform Infrared, Sulfur Oxides/*chemistry | 10.1016/s0162-0134(00)00081-7 | Phylogeny |
Enzymology | 11226874 | Cloning and expression of the catalase gene from the anaerobic bacterium Desulfovibrio vulgaris (Miyazaki F). | Kitamura M, Nakanishi T, Kojima S, Kumagai I, Inoue H | J Biochem | 2001 | Amino 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, Ultraviolet | 10.1093/oxfordjournals.jbchem.a002865 | Metabolism |
Enzymology | 11226881 | Purification 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 K | J Biochem | 2001 | Acetate 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/metabolism | 10.1093/oxfordjournals.jbchem.a002872 | Metabolism |
Metabolism | 12054869 | Redox-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 H | J Mol Biol | 2002 | Amino 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, Solutions | 10.1016/S0022-2836(02)00367-4 | Enzymology |
Metabolism | 12296727 | Structural 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 Y | J Am Chem Soc | 2002 | Binding 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, Raman | 10.1021/ja012645k | Enzymology |
Metabolism | 12381206 | Pulsed electron-electron double resonance on multinuclear metal clusters: assignment of spin projection factors based on the dipolar interaction. | Elsasser C, Brecht M, Bittl R | J Am Chem Soc | 2002 | Computer Simulation, Desulfovibrio vulgaris/enzymology, Electron Spin Resonance Spectroscopy, Fourier Analysis, Hydrogen/chemistry/metabolism, Hydrogenase/*chemistry/metabolism, Iron-Sulfur Proteins/*chemistry/metabolism, Models, Molecular | 10.1021/ja027348+ | Enzymology |
Enzymology | 12515509 | Single 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 W | J Am Chem Soc | 2003 | Bacterial Proteins/chemistry/metabolism, Binding Sites, Desulfovibrio vulgaris/*enzymology, Electron Spin Resonance Spectroscopy, Hydrogenase/*chemistry/metabolism, Models, Chemical, Models, Molecular, Oxidation-Reduction, Protein Conformation | 10.1021/ja027522u | Metabolism |
Enzymology | 12761175 | Cloning and expression of the superoxide dismutase gene from the obligate anaerobic bacterium Desulfovibrio vulgaris (Miyazaki F). | Nakanishi T, Inoue H, Kitamura M | J Biochem | 2003 | Amino 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/*genetics | 10.1093/jb/mvg051 | Metabolism |
Enzymology | 14570480 | Direct 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 W | J Am Chem Soc | 2003 | Computer Simulation, Cupriavidus necator/*enzymology, Electron Spin Resonance Spectroscopy/methods, Hydrogen/*chemistry, Hydrogen Bonding, Hydrogenase/*chemistry, Ligands, Models, Molecular, Oxidation-Reduction | 10.1021/ja036624x | |
Enzymology | 14581238 | Role 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 H | Biophys J | 2003 | Amino 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/*chemistry | 10.1016/S0006-3495(03)74756-0 | |
Enzymology | 14746912 | Cloning and expression of the enolase gene from Desulfovibrio vulgaris (Miyazaki F). | Kitamura M, Takayama Y, Kojima S, Kohno K, Ogata H, Higuchi Y, Inoue H | Biochim Biophys Acta | 2004 | Amino 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 Reaction | 10.1016/j.bbaexp.2003.11.008 | Metabolism |
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Enzymology | 15299378 | Location 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 S | Acta Crystallogr D Biol Crystallogr | 1994 | 10.1107/S0907444994002416 | ||
Genetics | 15323546 | Roles of noncoordinated aromatic residues in redox regulation of cytochrome c3 from Desulfovibrio vulgaris Miyazaki F. | Takayama Y, Harada E, Kobayashi R, Ozawa K, Akutsu H | Biochemistry | 2004 | Amino 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/genetics | 10.1021/bi049551i | Enzymology |
Enzymology | 15611882 | An 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 W | J Biol Inorg Chem | 2004 | Binding Sites, Carbon/chemistry/*metabolism, Desulfovibrio vulgaris/*enzymology, Electron Spin Resonance Spectroscopy, Hydrogenase/*chemistry/*metabolism, Nickel/chemistry/*metabolism, Spectrum Analysis | 10.1007/s00775-004-0613-5 | Metabolism |
Enzymology | 15667250 | EPR 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 W | Biochem Soc Trans | 2005 | Desulfovibrio vulgaris/*enzymology, Electron Spin Resonance Spectroscopy, Hydrogenase/*chemistry, Protein Conformation, Spectroscopy, Fourier Transform Infrared | 10.1042/BST0330007 | |
Enzymology | 16292669 | A 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 W | J Biol Inorg Chem | 2005 | Binding Sites, Crystallization, Cysteine/chemistry, Desulfovibrio vulgaris/*enzymology, Electron Spin Resonance Spectroscopy/methods, Hydrogenase/*chemistry/metabolism, Ligands, Oxidation-Reduction, Protein Conformation, Protons, Sulfur/chemistry | 10.1007/s00775-005-0048-7 | Metabolism |
Enzymology | 16460012 | Redox 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 H | Biochemistry | 2006 | Binding Sites, Cytochrome c Group/chemistry/*metabolism, Desulfovibrio vulgaris/*enzymology, Heme/metabolism, Hydrogenase/*metabolism, Kinetics, Magnetic Resonance Spectroscopy/methods, Methionine/chemistry/metabolism, Models, Molecular, Oxidation-Reduction | 10.1021/bi0514360 | Metabolism |
Enzymology | 16610917 | Hydrogen 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 W | J Phys Chem B | 2006 | Chemical Phenomena, Chemistry, Physical, Cysteine/chemistry, Desulfovibrio vulgaris/*enzymology, Electron Spin Resonance Spectroscopy, Histidine/chemistry, Hydrogen Bonding, Hydrogenase/*chemistry, Models, Molecular | 10.1021/jp0573902 | |
16887609 | Membrane-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 H | Anaerobe | 1997 | 10.1006/anae.1997.0114 | |||
Enzymology | 16893172 | Spectroelectrochemical characterization of the [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F. | Fichtner C, Laurich C, Bothe E, Lubitz W | Biochemistry | 2006 | Crystallography, X-Ray, Desulfovibrio vulgaris/*classification/*enzymology, Electrochemistry, Hydrogen-Ion Concentration, Hydrogenase/*chemistry, Oxidation-Reduction, Spectroscopy, Fourier Transform Infrared, Vibration | 10.1021/bi0602462 | Phylogeny |
Metabolism | 16902753 | Sequential and structural analysis of [NiFe]-hydrogenase-maturation proteins from Desulfovibrio vulgaris Miyazaki F. | Agrawal AG, Voordouw G, Gartner W | Antonie Van Leeuwenhoek | 2006 | Amino Acid Sequence, Bacterial Proteins/*chemistry/*metabolism, Desulfovibrio vulgaris/*genetics/*metabolism, Gene Expression Regulation, Bacterial, Gene Expression Regulation, Enzymologic, Hydrogenase/*metabolism, Molecular Sequence Data, Phylogeny | 10.1007/s10482-006-9082-x | Enzymology |
Metabolism | 17150519 | Application 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 Y | Nucleic Acids Symp Ser (Oxf) | 2004 | Bacterial Proteins/biosynthesis/*metabolism, Cell-Free System, Desulfovibrio vulgaris/*metabolism, Flavin Mononucleotide/*metabolism, Protein Binding, *Protein Biosynthesis, Time Factors | 10.1093/nass/48.1.143 | |
Enzymology | 17507210 | Superoxide radical sensing using a cytochrome c3 immobilized conducting polymer electrode. | Darain F, Park JS, Akutsu H, Shim YB | Biosens Bioelectron | 2007 | Biosensing 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/*analysis | 10.1016/j.bios.2007.03.026 | |
Phylogeny | 18607091 | Crystallization 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 Y | Acta Crystallogr Sect F Struct Biol Cryst Commun | 2008 | Bacterial Proteins/*chemistry/*classification/genetics, Crystallization, Desulfovibrio vulgaris/*chemistry/genetics, Gene Expression Regulation, Bacterial, Peptide Termination Factors/*chemistry/*classification/genetics, Sulfates/*chemistry/metabolism, X-Ray Diffraction | 10.1107/S1744309108015583 | Metabolism |
Metabolism | 18702516 | Strategic 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 H | Biochemistry | 2008 | Amino 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/physiology | 10.1021/bi8005708 | Enzymology |
Enzymology | 18765921 | Crystallization and preliminary X-ray crystallographic study of flavoredoxin from Desulfovibrio vulgaris Miyazaki F. | Ueda Y, Shibata N, Takeuchi D, Kitamura M, Higuchi Y | Acta Crystallogr Sect F Struct Biol Cryst Commun | 2008 | Crystallization, Crystallography, X-Ray, Desulfovibrio vulgaris/*chemistry, Flavoproteins/*chemistry/isolation & purification, Oxidoreductases/*chemistry/isolation & purification, Protein Structure, Tertiary | 10.1107/S1744309108025840 | Phylogeny |
18800855 | Simultaneous 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 N | J Phys Chem B | 2008 | Algorithms, 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 Factors | 10.1021/jp804130j | ||
Enzymology | 18997328 | Purification, 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 W | Acta Crystallogr Sect F Struct Biol Cryst Commun | 2008 | Bacterial 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 Diffraction | 10.1107/S1744309108029588 | Phylogeny |
Enzymology | 19151100 | Cloning and expression of the MutM gene from obligate anaerobic bacterium Desulfovibrio vulgaris (Miyazaki F). | Sanada H, Nakanishi T, Inoue H, Kitamura M | J Biochem | 2009 | Anaerobiosis, 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, Atomic | 10.1093/jb/mvp005 | Metabolism |
Metabolism | 19626348 | Probing 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 W | J Biol Inorg Chem | 2009 | Bacterial 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 Infrared | 10.1007/s00775-009-0566-9 | Enzymology |
Metabolism | 19708087 | Structure 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 Y | FEBS J | 2009 | Amino 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/metabolism | 10.1111/j.1742-4658.2009.07184.x | Enzymology |
Enzymology | 19759926 | [NiFe] hydrogenases: structural and spectroscopic studies of the reaction mechanism. | Ogata H, Lubitz W, Higuchi Y | Dalton Trans | 2009 | Biocatalysis, Carbon Monoxide/pharmacology, Enzyme Inhibitors/pharmacology, Hydrogenase/antagonists & inhibitors/*chemistry/*metabolism, Oxidation-Reduction, Spectrum Analysis | 10.1039/b903840j | Metabolism |
Enzymology | 19845323 | Spectroelectrochemical 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 I | J Phys Chem B | 2009 | Argon/chemistry, Catalytic Domain, Desulfovibrio vulgaris/*enzymology, *Electrochemical Techniques, Electrodes, Enzymes, Immobilized/chemistry/metabolism, Gold/*chemistry, Hydrogen/chemistry, Hydrogenase/*chemistry/metabolism, Oxidation-Reduction, *Spectrophotometry, Infrared | 10.1021/jp906575r | Metabolism |
Enzymology | 19925776 | Inhibition 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 W | Biochim Biophys Acta | 2009 | Antimetabolites/*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 Infrared | 10.1016/j.bbabio.2009.11.002 | Metabolism |
Enzymology | 20165762 | Comparison 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 R | Phys Chem Chem Phys | 2010 | Catalytic Domain, Cupriavidus necator/*enzymology, Desulfovibrio vulgaris/*enzymology, Electron Spin Resonance Spectroscopy, Hydrogen Bonding, Hydrogenase/*chemistry, Oxidation-Reduction, Spin Labels | 10.1039/b922236g | |
Enzymology | 20221530 | Concerto catalysis--harmonising [NiFe]hydrogenase and NiRu model catalysts. | Ichikawa K, Nonaka K, Matsumoto T, Kure B, Yoon KS, Higuchi Y, Yagi T, Ogo S | Dalton Trans | 2010 | Bacterial Proteins/chemistry/*metabolism, *Catalysis, Desulfovibrio vulgaris/enzymology, Hydrogen/chemistry, Hydrogen-Ion Concentration, Hydrogenase/chemistry/*metabolism, Models, Molecular, Protein Conformation, Ruthenium/*chemistry | 10.1039/b926061g | Metabolism |
Enzymology | 20301175 | Intermediates in the catalytic cycle of [NiFe] hydrogenase: functional spectroscopy of the active site. | Pandelia ME, Ogata H, Lubitz W | Chemphyschem | 2010 | Biocatalysis, Catalytic Domain, Electron Spin Resonance Spectroscopy, Hydrogenase/*chemistry/metabolism, Oxidation-Reduction, Protein Structure, Tertiary, Spectroscopy, Fourier Transform Infrared | 10.1002/cphc.200900950 | Metabolism |
20397678 | Effects 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 F | J Phys Chem B | 2010 | Carrier Proteins, Crystallography, X-Ray, Flavin Mononucleotide/*chemistry, Fluorescence, Hydrogen Bonding, X-Ray Diffraction | 10.1021/jp912137s | ||
Enzymology | 20449009 | FTIR 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 W | Phys Chem Chem Phys | 2009 | Catalytic Domain, Desulfovibrio vulgaris/*enzymology, Deuterium/*chemistry, Hydrogen/*chemistry, Hydrogenase/*chemistry/metabolism, Kinetics, *Light, Models, Molecular, Photochemistry, *Protons, Spectroscopy, Fourier Transform Infrared, Temperature, Water/chemistry | 10.1039/b913635e | Metabolism |
Enzymology | 21045297 | Purification, 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 W | Acta Crystallogr Sect F Struct Biol Cryst Commun | 2010 | Crystallization, Crystallography, X-Ray, Desulfovibrio vulgaris/*enzymology, Hydrogensulfite Reductase/*chemistry/isolation & purification, Models, Molecular, Protein Structure, Tertiary | 10.1107/S1744309110033191 | Phylogeny |
21347481 | Simultaneous 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 F | Phys Chem Chem Phys | 2011 | Amino Acid Substitution, Bacterial Proteins/*chemistry, Flavoproteins/*chemistry, Isomerism, Models, Molecular, Molecular Dynamics Simulation, Photochemistry | 10.1039/c0cp02634d | ||
Enzymology | 23053531 | Computational 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 F | J Biol Inorg Chem | 2012 | Carbon/*chemistry, Coordination Complexes/*chemistry, *Electrons, Hydrogenase/*chemistry, Magnetics, Models, Molecular, Nickel/*chemistry, *Quantum Theory | 10.1007/s00775-012-0941-9 | |
Enzymology | 23159801 | Photosensitivity 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 S | Biochem Biophys Res Commun | 2012 | Desulfovibrio vulgaris/*enzymology, Hydrogenase/chemistry/*radiation effects, Iron/chemistry, *Light, Nickel/chemistry, *Photochemical Processes, Spectroscopy, Fourier Transform Infrared | 10.1016/j.bbrc.2012.10.136 | |
Enzymology | 23201506 | Novel H2-oxidizing [NiFeSe]hydrogenase from Desulfovibrio vulgaris Miyazaki F. | Nonaka K, Nguyen NT, Yoon KS, Ogo S | J Biosci Bioeng | 2012 | Amino Acid Sequence, Biocatalysis, Desulfovibrio vulgaris/*enzymology/genetics, Hydrogenase/chemistry/genetics/*metabolism, Molecular Sequence Data, Oxidation-Reduction, Sequence Alignment | 10.1016/j.jbiosc.2012.10.011 | Genetics |
Enzymology | 23215250 | Effect 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 MA | Langmuir | 2013 | Adsorption, 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, Thermodynamics | 10.1021/la303635q | |
Enzymology | 24038675 | Spectroscopic 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 HS | Chembiochem | 2013 | Desulfovibrio vulgaris/*enzymology, Electrochemical Techniques, Electron Spin Resonance Spectroscopy, Electron Transport, Electrons, Hydrogenase/*chemistry/metabolism, Oxidation-Reduction, Spectroscopy, Fourier Transform Infrared, Temperature | 10.1002/cbic.201300120 | Metabolism |
24108633 | Photoinduced electron transfer modeling to simulate flavoprotein fluorescence decay. | Nunthaboot N, Lugsanangarm K, Nueangaudom A, Pianwanit S, Kokpol S, Tanaka F | Methods Mol Biol | 2014 | Carrier Proteins/chemistry, Desulfovibrio vulgaris/chemistry, Electron-Transferring Flavoproteins/*chemistry, Flavin Mononucleotide/chemistry, *Fluorescence, Molecular Dynamics Simulation, Photochemistry/methods, Solutions/chemistry, Tryptophan/*chemistry, Tyrosine/chemistry | 10.1007/978-1-62703-649-8_14 | ||
Metabolism | 25773195 | Surface display of highly-stable Desulfovibrio vulgaris carbonic anhydrase on polyester beads for CO2 capture. | Hooks DO, Rehm BH | Biotechnol Lett | 2015 | Bacterial 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/*metabolism | 10.1007/s10529-015-1803-7 | Enzymology |
Enzymology | 25898020 | FT-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 S | J Phys Chem B | 2015 | Desulfovibrio vulgaris/*enzymology, Electron Spin Resonance Spectroscopy, Hydrogenase/*chemistry/metabolism, *Light, Nickel/*chemistry/metabolism, Organometallic Compounds/*chemistry/metabolism, Spectroscopy, Fourier Transform Infrared, Thermodynamics | 10.1021/acs.jpcb.5b03075 | Metabolism |
Enzymology | 26259066 | Hydride 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 SP | Nat Commun | 2015 | Desulfovibrio vulgaris/*enzymology, Hydrogenase/*chemistry, Magnetic Resonance Spectroscopy | 10.1038/ncomms8890 | |
Enzymology | 26277806 | Light-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 T | J Phys Chem Lett | 2014 | 10.1021/jz5008164 | Biotechnology | |
Enzymology | 27456760 | Photoactivation 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 S | Phys Chem Chem Phys | 2016 | Desulfovibrio vulgaris/*enzymology, Hydrogenase/*metabolism, Light, Photochemistry | 10.1039/c6cp04628b | Phylogeny |
27857559 | Roles 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 H | Biophysics (Nagoya-shi) | 2006 | 10.2142/biophysics.2.45 | |||
Enzymology | 28192203 | Electrostatic 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 K | Biochim Biophys Acta Proteins Proteom | 2017 | Cell 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 Electricity | 10.1016/j.bbapap.2017.02.009 | Metabolism |
Enzymology | 29753939 | Reactivation 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 K | Bioelectrochemistry | 2018 | Biocatalysis, 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/chemistry | 10.1016/j.bioelechem.2018.05.003 | Metabolism |
Enzymology | 30609080 | New 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 Y | Protein Sci | 2019 | Catalysis, Catalytic Domain, Desulfovibrio vulgaris/*enzymology, Enzyme Assays/*methods, Gases/chemistry/metabolism, Hydrogen/*chemistry/metabolism, Hydrogenase/chemistry/*metabolism, Spectrum Analysis, Raman/*methods | 10.1002/pro.3569 | Metabolism |
Enzymology | 31354654 | H2 Kinetic Isotope Fractionation Superimposed by Equilibrium Isotope Fractionation During Hydrogenase Activity of D. vulgaris Strain Miyazaki. | Loffler M, Kummel S, Vogt C, Richnow HH | Front Microbiol | 2019 | 10.3389/fmicb.2019.01545 | ||
Enzymology | 33021496 | Towards 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 Y | Acta Crystallogr D Struct Biol | 2020 | Crystallography/*methods, Desulfovibrio vulgaris/enzymology, Freezing, Hydrogenase/*chemistry, Models, Molecular, Neutron Diffraction/*methods | 10.1107/S2059798320011365 |
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