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Information on EC 1.12.2.1 - cytochrome-c3 hydrogenase and Organism(s) Desulfovibrio vulgaris and UniProt Accession Q06173
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1.12.2.1 cytochrome-c3 hydrogenaseIUBMB Comments
An iron-sulfur protein. Some forms of the enzyme contain nickel ([NiFe]-hydrogenases) and, of these, some contain selenocysteine ([NiFeSe]-hydrogenases). Methylene blue and other acceptors can also be reduced.
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Word Map
- 1.12.2.1
- hydrogenases
- desulfovibrio
- nickel
-
hydride
- eutropha
-
h-cluster
-
iron-sulfur
- ralstonia
-
o2-tolerant
- nife-hydrogenases
- hildenborough
-
dihydrogen
-
hyperfine
-
electrochemistry
-
diiron
-
sulfate-reducing
- fe-hydrogenase
- miyazaki
-
heterolytic
- desulfuricans
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oxygen-tolerant
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electrocatalytic
-
allochromatium
-
metallochaperone
-
overpotential
-
subcluster
- pasteurianum
- fructosovorans
-
organometallic
- hydf
-
dinuclear
-
bimetallic
-
co-inhibited
-
nickel-iron
- vinosum
-
h2-oxidizing
-
hydrogen-producing
-
maturase
- environmental protection
- fhl
-
tetraheme
- industry
-
metallocenter
- hydrogenlyase
-
hyscore
-
nickel-binding
- synthesis
-
h2-dependent
-
electrocatalysts
The taxonomic range for the selected organisms is: Desulfovibrio vulgaris
The expected taxonomic range for this enzyme is: Bacteria, Archaea
The expected taxonomic range for this enzyme is: Bacteria, Archaea
Synonyms
[nife] hydrogenase, [nife]-hydrogenase, [fefe] hydrogenase, [fe]-hydrogenase, [fe] hydrogenase, h2ase, fe-only hydrogenase, [nifese] hydrogenase, hydab, [nifese] hase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
cytochrome c3 hydrogenase
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-
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cytochrome c3 reductase
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-
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cytochrome hydrogenase
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-
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H2:ferricytochrome c3 oxidoreductase
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-
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hydrogenase
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-
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hydrogenase, cytochrome
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-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
redox reaction
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-
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oxidation
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-
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reduction
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-
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PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
hydrogen:ferricytochrome-c3 oxidoreductase
An iron-sulfur protein. Some forms of the enzyme contain nickel ([NiFe]-hydrogenases) and, of these, some contain selenocysteine ([NiFeSe]-hydrogenases). Methylene blue and other acceptors can also be reduced.
CAS REGISTRY NUMBER
COMMENTARY
9027-05-8
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9079-91-8
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
Fe(III)-nitrilotriacetate + ferricytochrome c3
Fe(II)-nitrilotriacetate + ferrocytochrome c3
-
-
-
-
?
H2 + ferricytochrome Hmc
H+ + ferrocytochrome Hmc
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13 kDa tetraheme cytochrome c3 forms a complex with a hexadecaheme high molecular weight cytochrome c, i.e. Hmc
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-
r
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
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-
-
-
?
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
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part of an electron transport chain that mediates electronic coupling between periplasmic hydrogen oxidation and cytosolic sulfate reduction
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-
r
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
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13 kDa tetraheme cytochrome c3 forms a complex with a hexadecaheme high molecular weight cytochrome c, i.e. Hmc
-
-
r
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
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the positive charges of Lys60, Lys72, Lys95, and Lys101 around heme 4 are important for formation of the transient complex with [NiFe] hydrogenase in the initial stage of the cytochrome c3 reduction. Reaction with wild-type and mutant cytochrome c3
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-
?
additional information
?
-
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enzyme reduces soluble uranium(VI) with ferrocytochrome c3 as electron donor to uranium(IV) forming the insoluble mineral uraninite, this reaction is impaired in a cytochrome c3 mutant strain
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-
?
additional information
?
-
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the enzyme catalyzes the conversion of para-H2 to normal H2 over D2O as well as the isotope exchange reaction in the H2D2O system
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-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
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part of an electron transport chain that mediates electronic coupling between periplasmic hydrogen oxidation and cytosolic sulfate reduction
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-
r
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
cytochrome c3
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the electron transfer between [NiFeSe] hydrogenase and octaheme cytochrome c3 is activated by tetraheme cytochrome c3, cytochrome c3 can acts as an electron shuttle between hydrogenase and polyheme cytochromes
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Fe
Iron
Ni
Nickel
Se
Iron
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iron-sulfur protein, 7-9 iron atoms and 7-8 labile sulfide ions
Iron
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the active site is composed of a binuclear Ni-Fe complex bearing three diatomic nonprotein ligands to Fe and three bridges between the two metals, two of which are thiolate side chains of the protein moiety. The third bridging atom in the enzyme is suggested to be sulfur species. The bridging atom is liberated as H2S when the enzyme is reduced under H2 in the presence of its electron carrier cytochrome c3 or methyl viologen
Iron
-
12.5 gatom nonheme iron and 11.5 gatom of acid-labile sulfide per mol, arranged in at least two Fe4S4 clusters of the ferredoxin type
Nickel
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the active site is composed of a binuclear Ni-Fe complex bearing three diatomic nonprotein ligands to Fe and three bridges between the two metals, two of which are thiolate side chains of the protein moiety. The third bridging atom in the enzyme is suggested to be sulfur species. The bridging atom is liberated as H2S when the enzyme is reduced under H2 in the presence of its electron carrier cytochrome c3 or methyl viologen
Nickel
-
purified enzyme contains variable amounts of nickel, ranging from 0.1 to 0.6 gatom per mol of enzyme
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Phospholipid
-
H2-production from reduced methyl viologen requires phospholipids
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0099
mutant cytochrome c3 K101M
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25°C, pH 7.0, mutant cytochrome c3 K101M
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0.0027
mutant cytochrome c3 K10M
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25°C, pH 7.0, mutant cytochrome c3 K10M
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0.0045
mutant cytochrome c3 K15M
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25°C, pH 7.0, mutant cytochrome c3 K15M
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0.003
mutant cytochrome c3 K26M
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25°C, pH 7.0, mutant cytochrome c3 K26M
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0.0051
mutant cytochrome c3 K57M
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25°C, pH 7.0, mutant cytochrome c3 K57M
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0.0057
mutant cytochrome c3 K58M
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25°C, pH 7.0, mutant cytochrome c3 K58M
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0.0104
mutant cytochrome c3 K60M
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25°C, pH 7.0, mutant cytochrome c3 K60M
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0.0067
mutant cytochrome c3 K72M
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25°C, pH 7.0, mutant cytochrome c3 K72M
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0.0057
mutant cytochrome c3 K94M
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25°C, pH 7.0, mutant cytochrome c3 K94M
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0.0073
mutant cytochrome c3 K95M
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25°C, pH 7.0, mutant cytochrome c3 K95M
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0.0022
mutant cytochrome c3 Y65A
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25°C, pH 7.0, mutant cytochrome c3 Y65A
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0.0043
mutant cytochrome c3 Y66L
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25°C, pH 7.0, mutant cytochrome c3 Y66L
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0.032
[Fe] hydrogenase-cytochrome c3 complex
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pH 7.0, electron transfer kinetics
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0.006
[Fe] hydrogenase-cytochrome c3-cytochrome Hmc complex
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pH 7.0, electron transfer kinetics
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0.04
[Fe] hydrogenase-cytochrome Hmc complex
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pH 7.0, electron transfer kinetics
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additional information
additional information
-
steady-state kinetics of the enzymatic reaction, kinetics of electron transfer between cytochrome c Hmc and cytochrome c3, sigmoidal kinetics for cytochrome c3 reduction
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
462
[Fe] hydrogenase-cytochrome c3 complex
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pH 7.0, electron transfer kinetics
-
2.3
[Fe] hydrogenase-cytochrome c3-cytochrome Hmc complex
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pH 7.0, electron transfer kinetics
-
0.15
[Fe] hydrogenase-cytochrome Hmc complex
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pH 7.0, electron transfer kinetics
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
Ki for CO is 8.9 Torr
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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of lactate/sulfate grown cells. The enzyme is present in the cell in two states: the majority is membrane-associated (the [NiFeSe]m form) and a minor amount is soluble (the [NiFeSe]s form)
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of lactate/sulfate grown cells. The enzyme is present in the cell in two states: the majority is membrane-associated (the [NiFeSe]m form) and a minor amount is soluble (the [NiFeSe]s form)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
lipoprotein
lipoprotein
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post-translationally modified, probably by the binding of a lipidic group at the N-terminus. The presence of such a group explains the membrane association of the enzyme, the requirement of phospholipids for maximal activity, and the blockage of the large subunit to N-terminal sequencing
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystallization by vapor diffusion method with polyethylene glycol or 2-methyl-2,4-pentanediol as precipitating agents. Seeding procedure is necessary to grow an X-ray grade crystal
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ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
long exposure of the oxidized enzyme to oxygen does not irreversibly inactivate the hydrogenase. In the reduced form the hydrogenase is irreveribly inactivated
-
395559
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
environmental protection
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enzyme might be useful in development of a mechanism to remove contaminating uranium from groundwaters
synthesis
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adsorption of cytochrome c3 at a pyrolytic graphite electrode is observed in the room-temperature ionic liquids 1-butyl-3-methylimidazolium tetrafluoroborate, 1-ethyl-3-methylimidazolium tetrafluoroborate and 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide. The electrochemical signal differs however from that obtained in aqueous buffer, and depended on the type of room-temperature ionic liquids. 1-Ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide, as a hydrophobic non-water-miscible room-temperature ionic liquids, stabilizes the native form of cytochrome c3 and allows an amount of electroactive protein 30fold higher than observed in aqueous buffer. Catalytic oxidation of H2 via [NiFe] hydrogenase mediated by cytochrome c33 fails however, possibly due to inhibition of the hydrogenase in presence of room-temperature ionic liquids
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Odom, J.M.; Peck, H.D.
Hydrogenase, electron-transfer proteins, and energy coupling in the sulfate-reducing bacteria Desulfovibrio
Annu. Rev. Microbiol.
38
551-592
1984
Desulfovibrio desulfuricans, Desulfovibrio desulfuricans Norway 4, Desulfovibrio vulgaris, Desulfovibrio vulgaris Hildenborough, Megalodesulfovibrio gigas
Yagi, T.; Kimura, K.; Daidoji, H.; Sakai, F.; Tamura, S.; Inokuchi, H.
Properties of purified hydrogenase from the particulate fraction of Desulfovibrio vulgaris, Miyazaki
J. Biochem.
79
661-671
1976
Desulfovibrio vulgaris, Desulfovibrio vulgaris Miyazaki
Grande, H.J.; van Berkel-Arts, A.; Bregh, J.; van Dijk, K.; Veeger, C.
Kinetic properties of hydrogenase isolated from Desulfovibrio vulgaris (Hildenborough)
Eur. J. Biochem.
131
81-88
1983
Desulfovibrio vulgaris
Higuchi, Y.; Yasuoka, N.; Kakudo, M.; Katsube, Y.; Yagi, T.; Inokuchi, H.
Single crystals of hydrogenase from Desulfovibrio vulgaris Miyazaki F
J. Biol. Chem.
262
2823-2825
1987
Desulfovibrio vulgaris
Aubert, C.; Brugna, M.; Dolla, A.; Bruschi, M.; Giudici-Orticoni, M.T.
A sequential electron transfer from hydrogenases to cytochromes in sulfate-reducing bacteria
Biochim. Biophys. Acta
1476
85-92
2000
Desulfomicrobium norvegicum, Desulfovibrio vulgaris, Desulfovibrio vulgaris Hildenborough
Higuchi, Y.; Yagi, T.
Liberation of hydrogen sulfide during the catalytic action of Desulfovibrio hydrogenase under the atmosphere of hydrogen
Biochem. Biophys. Res. Commun.
255
295-299
1999
Desulfovibrio vulgaris, Desulfovibrio vulgaris Miyazaki
Payne, R.B.; Gentry, D.M.; Rapp-Giles, B.J.; Casalot, L.; Wall, J.D.
Uranium reduction by Desulfovibrio desulfuricans strain G20 and a cytochrome c3 mutant
Appl. Environ. Microbiol.
68
3129-3132
2002
Desulfovibrio desulfuricans, Desulfovibrio vulgaris, Desulfovibrio vulgaris Hildenborough
Guiral, M.; Leroy, G.; Bianco, P.; Gallice, P.; Guigliarelli, B.; Bruschi, M.; Nitschke, W.; Giudici-Orticoni, M.T.
Interaction and electron transfer between the high molecular weight cytochrome and cytochrome c3 from Desulfovibrio vulgaris Hildenborough: kinetic, microcalorimetric, EPR and electrochemical studies
Biochim. Biophys. Acta
1723
45-54
2005
Desulfovibrio vulgaris, Desulfovibrio vulgaris Hildenborough
Pereira, P.M.; Teixeira, M.; Xavier, A.V.; Louro, R.O.; Pereira, I.A.
The Tmc complex from Desulfovibrio vulgaris hildenborough is involved in transmembrane electron transfer from periplasmic hydrogen oxidation
Biochemistry
45
10359-10367
2006
Desulfovibrio vulgaris, Desulfovibrio vulgaris Hildenborough
Yahata, N.; Saitoh, T.; Takayama, Y.; Ozawa, K.; Ogata, H.; Higuchi, Y.; Akutsu, H.
Redox interaction of cytochrome c3 with [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F
Biochemistry
45
1653-1662
2006
Desulfovibrio vulgaris, Desulfovibrio vulgaris Miyazaki F
Vignais, P.M.
H/D exchange reactions and mechanistic aspects of the hydrogenases
Coord. Chem. Rev.
249
1677-1690
2005
Desulfovibrio vulgaris, Desulfovibrio vulgaris Miyazaki
-
Valente, F.M.; Oliveira, A.S.; Gnadt, N.; Pacheco, I.; Coelho, A.V.; Xavier, A.V.; Teixeira, M.; Soares, C.M.; Pereira, I.A.
Hydrogenases in Desulfovibrio vulgaris Hildenborough: structural and physiologic characterisation of the membrane-bound [NiFeSe] hydrogenase
J. Biol. Inorg. Chem.
10
667-682
2005
Desulfovibrio vulgaris, Desulfovibrio vulgaris Hildenborough
Park, H.S.; Lin, S.; Voordouw, G.
Ferric iron reduction by Desulfovibrio vulgaris Hildenborough wild type and energy metabolism mutants
Antonie van Leeuwenhoek
93
79-85
2007
Desulfovibrio vulgaris, Desulfovibrio vulgaris Hildenborough
Valente, F.M.; Pereira, P.M.; Venceslau, S.S.; Regalla, M.; Coelho, A.V.; Pereira, I.A.
The [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough is a bacterial lipoprotein lacking a typical lipoprotein signal peptide
FEBS Lett.
581
3341-3344
2007
Desulfovibrio vulgaris, Desulfovibrio vulgaris Hildenborough
Iida, S.; Asakura, N.; Tabata, K.; Okura, I.; Kamachi, T.
Role of positive charge of lysine residue on cytochrome c3 for electrostatic interaction with hydrogenase
J. Porphyr. Phthalocyanines
11
66-73
2007
Desulfovibrio vulgaris
-
Ciaccafava, A.; Alberola, M.; Hameury, S.; Infossi, P.; Giudici-Orticoni, M.; Lojou, E.
Hydrogen bioelectrooxidation in ionic liquids: From cytochrome c 3 redox behavior to hydrogenase activity
Electrochim. Acta
56
3359-3368
2011
Desulfovibrio vulgaris, Desulfovibrio vulgaris Hildenborough
-
Sugimoto, Y.; Kitazumi, Y.; Shirai, O.; Nishikawa, K.; Higuchi, Y.; Yamamoto, M.; Kano, K.
Electrostatic roles in electron transfer from [NiFe] hydrogenase to cytochrome c3 from Desulfovibrio vulgaris Miyazaki F
Biochim. Biophys. Acta
1865
481-487
2017
Desulfovibrio vulgaris, Desulfovibrio vulgaris Miyazaki F
Yagi, T.; Ogo, S.; Higuchi, Y.
Catalytic cycle of cytochrome-c3 hydrogenase, a [NiFe]-enzyme, deduced from the structures of the enzyme and the enzyme mimic
Int. J. Hydrogen Energy
39
18543-18550
2014
Desulfovibrio vulgaris (P21853), Desulfovibrio vulgaris Miyazaki F (P21853)
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