Nitratidesulfovibrio vulgaris (DSM 19637, Miyazaki F, JCM 14930)

Name: Nitratidesulfovibrio vulgaris (DSM 19637, Miyazaki F, JCM 14930)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 4163

Type strain

Strain Designation Miyazaki F

Culture col. no. DSM 19637 Miyazaki F JCM 14930

NCBI tax ID(s) 881

Special Collections DSMZ JCM

History DSMZ <- J. D. Wall, University of Calgary, Canada; (Desulfovibrio vulgaris) <- H. Akutsu, Yokohama National University, Japan; <- S. Iwasaki, Ajinomoto Company, Inc., Central Research Laboratories, Kawasaki, Japan; Miyazaki F {1949} JCM <-- H. Akutsu <-- S. Iwasaki strain Miyazaki F.

Links

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

anaerobe genome sequence Bacteria

Name and taxonomic classification

SI-ID 402991

DSM 19637

@ref 20215

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

Domain Bacteria

Phylum Thermodesulfobacteriota

Class Desulfovibrionia

Order Desulfovibrionales

Family Desulfovibrionaceae

Genus Nitratidesulfovibrio

Species Nitratidesulfovibrio vulgaris

Full scientific name Nitratidesulfovibrio vulgaris (Postgate and Campbell 1966) Waite et al. 2020

Synonyms (1)

Desulfovibrio vulgaris

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8227	DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641)		Medium recipe at MediaDive	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 (°C)
8227	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

8227

Oxygen toleranceanaerobe

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Mud (Sludge)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
8227	degraded paddy field	Miyazaki	Japan	JPN	Asia
67770	Paddy field soil in Miyazaki		Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8227	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2138v1 assembly for Nitratidesulfovibrio vulgaris str. 'Miyazaki F'	complete	GCA_000021385	883.4	643348539	883	24.76

GC content

@ref	GC-content (mol%)	Method
8227	67	sequence analysis

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	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	10.1107/S2059798320011365	2020
Enzymology	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	10.3389/fmicb.2019.01545	2019
Enzymology	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	10.1002/pro.3569	2019
Enzymology	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	10.1016/j.bioelechem.2018.05.003	2018
Enzymology	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	10.1016/j.bbapap.2017.02.009	2017
Enzymology	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	10.1039/c6cp04628b	2016
Enzymology	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	10.1021/jz5008164	2014
Enzymology	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	10.1038/ncomms8890	2015
Enzymology	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	10.1021/acs.jpcb.5b03075	2015
Metabolism	Surface display of highly-stable Desulfovibrio vulgaris carbonic anhydrase on polyester beads for CO2 capture.	Hooks DO, Rehm BH	Biotechnol Lett	10.1007/s10529-015-1803-7	2015
	Photoinduced electron transfer modeling to simulate flavoprotein fluorescence decay.	Nunthaboot N, Lugsanangarm K, Nueangaudom A, Pianwanit S, Kokpol S, Tanaka F	Methods Mol Biol	10.1007/978-1-62703-649-8_14	2014
Enzymology	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	10.1002/cbic.201300120	2013
Enzymology	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	10.1021/la303635q	2013
Enzymology	Novel H2-oxidizing [NiFeSe]hydrogenase from Desulfovibrio vulgaris Miyazaki F.	Nonaka K, Nguyen NT, Yoon KS, Ogo S	J Biosci Bioeng	10.1016/j.jbiosc.2012.10.011	2012
Enzymology	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	10.1016/j.bbrc.2012.10.136	2012
Enzymology	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	10.1007/s00775-012-0941-9	2012
	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	10.1039/c0cp02634d	2011
Enzymology	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	10.1039/b913635e	2009
	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	10.1021/jp912137s	2010
Enzymology	Intermediates in the catalytic cycle of [NiFe] hydrogenase: functional spectroscopy of the active site.	Pandelia ME, Ogata H, Lubitz W	Chemphyschem	10.1002/cphc.200900950	2010
Enzymology	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	10.1039/b926061g	2010
Enzymology	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	10.1039/b922236g	2010
Enzymology	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	10.1016/j.bbabio.2009.11.002	2009
Enzymology	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	10.1021/jp906575r	2009
Enzymology	[NiFe] hydrogenases: structural and spectroscopic studies of the reaction mechanism.	Ogata H, Lubitz W, Higuchi Y	Dalton Trans	10.1039/b903840j	2009
Metabolism	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	10.1111/j.1742-4658.2009.07184.x	2009
Metabolism	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	10.1007/s00775-009-0566-9	2009
Enzymology	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	10.1093/jb/mvp005	2009
Enzymology	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	10.1107/S1744309108029588	2008
	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	10.1021/jp804130j	2008
Enzymology	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	10.1107/S1744309108025840	2008
Metabolism	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	10.1021/bi8005708	2008
Phylogeny	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	10.1107/S1744309108015583	2008
Enzymology	Superoxide radical sensing using a cytochrome c3 immobilized conducting polymer electrode.	Darain F, Park JS, Akutsu H, Shim YB	Biosens Bioelectron	10.1016/j.bios.2007.03.026	2007
Metabolism	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)	10.1093/nass/48.1.143	2004
Enzymology	Spectroelectrochemical characterization of the [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F.	Fichtner C, Laurich C, Bothe E, Lubitz W	Biochemistry	10.1021/bi0602462	2006
	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	10.1006/anae.1997.0114	1997
	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)	10.2142/biophysics.2.45	2006
Enzymology	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	10.1021/jp0573902	2006
Enzymology	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	10.1021/bi0514360	2006
Enzymology	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	10.1007/s00775-005-0048-7	2005
Enzymology	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	10.1042/BST0330007	2005
Enzymology	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	10.1007/s00775-004-0613-5	2004
Genetics	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	10.1021/bi049551i	2004
	Crystallization 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 N	Protein Pept Lett	10.2174/0929866043478428	2004
Enzymology	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	10.1016/j.bbaexp.2003.11.008	2004
Enzymology	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	10.1016/S0006-3495(03)74756-0	2003
Enzymology	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	10.1021/ja036624x	2003
Enzymology	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	10.1093/jb/mvg051	2003
Enzymology	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	10.1021/ja027522u	2003
Metabolism	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	10.1021/ja027348+	2002
Metabolism	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	10.1021/ja012645k	2002
Enzymology	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	10.1093/oxfordjournals.jbchem.a002872	2001
Enzymology	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	10.1093/oxfordjournals.jbchem.a002865	2001
Enzymology	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	10.1016/s0162-0134(00)00081-7	2000
Metabolism	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	10.1128/AEM.66.9.4168-4171.2000	2000
Enzymology	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	10.1007/pl00010654	2000
Enzymology	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	10.1128/JB.182.8.2200-2206.2000	2000
	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	10.1107/s0907444900000111	2000
Metabolism	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	10.1016/s0969-2126(99)80071-9	1999
Metabolism	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	10.1107/s0907444999003169	1999
Genetics	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	10.1107/s0907444998011810	1999
Metabolism	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	10.1016/S0006-3495(98)74067-6	1998
Enzymology	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	10.1093/oxfordjournals.jbchem.a022021	1998
Enzymology	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	10.1016/s0167-4781(96)00203-5	1997
Enzymology	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	10.1111/j.1348-0421.1995.tb02172.x	1995
Enzymology	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	10.1107/S0907444994002416	1994
Enzymology	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	S0021-9258(17)37499-9	1994
Enzymology	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	10.1016/0005-2728(92)90003-k	1992
Metabolism	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	10.1007/BF01875520	1991
Enzymology	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	10.1093/oxfordjournals.jbchem.a123269	1990
Phylogeny	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	10.1093/oxfordjournals.jbchem.a123267	1990
Metabolism	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	10.1021/bi00461a008	1990
Enzymology	Single crystals of hydrogenase from Desulfovibrio vulgaris Miyazaki F.	Higuchi Y, Yasuoka N, Kakudo M, Katsube Y, Yagi T, Inokuchi H	J Biol Chem	S0021-9258(18)61580-7	1987
Metabolism	Pyruvate dehydrogenase and the path of lactate degradation in Desulfovibrio vulgaris Miyazaki F.	Ogata M, Yagi T	J Biochem	10.1093/oxfordjournals.jbchem.a121717	1986
Enzymology	Magnetic susceptibility of hydrogenase from Desulfovibrio vulgaris.	Kimura K, Inokuchi H, Nanami H, Yagi T	J Biochem	10.1093/oxfordjournals.jbchem.a135246	1985
Enzymology	Purification and properties of thiosulfate reductase from Desulfovibrio vulgaris, Miyazaki F.	Aketagawa J, Kobayashi K, Ishimoto M	J Biochem	10.1093/oxfordjournals.jbchem.a135144	1985
Enzymology	Analysis of the active center of hydrogenase from Desulfovibrio vulgaris Miyazaki by magnetic measurements.	Yagi T, Kimura K, Inokuchi H	J Biochem	10.1093/oxfordjournals.jbchem.a135042	1985
Phylogeny	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
Enzymology	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	10.1107/S1744309110033191	2010
Metabolism	Sequential and structural analysis of [NiFe]-hydrogenase-maturation proteins from Desulfovibrio vulgaris Miyazaki F.	Agrawal AG, Voordouw G, Gartner W	Antonie Van Leeuwenhoek	10.1007/s10482-006-9082-x	2006
Metabolism	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	10.1016/S0022-2836(02)00367-4	2002
Enzymology	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	10.1021/bi00039a044	1995
Metabolism	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	10.1006/jmbi.1993.1620	1993
Metabolism	Structural studies of Desulfovibrio vulgaris ferrocytochrome c3 by two-dimensional NMR.	Turner DL, Salgueiro CA, LeGall J, Xavier AV	Eur J Biochem	10.1111/j.1432-1033.1992.tb17497.x	1992
	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	10.1016/0014-5793(92)80963-h	1992
Enzymology	Cloning and sequencing of a [NiFe] hydrogenase operon from Desulfovibrio vulgaris Miyazaki F.	Deckers HM, Wilson FR, Voordouw G	J Gen Microbiol	10.1099/00221287-136-10-2021	1990
Enzymology	Characterization of periplasmic hydrogenase from Desulfovibrio vulgaris Miyazaki K.	Aketagawa J, Kobayashi K, Ishimoto M	J Biochem	10.1093/jb/93.3.755	1983

References

#8227	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19637
#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Content

About us

Nitratidesulfovibrio vulgaris (DSM 19637, Miyazaki F, JCM 14930)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000021385

GC content

Genome-based predictions

Literature

Literature

References

BacDive

Help

Social Media