Information on EC 1.12.2.1 - cytochrome-c3 hydrogenase

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota

EC NUMBER
COMMENTARY
1.12.2.1
-
RECOMMENDED NAME
GeneOntology No.
cytochrome-c3 hydrogenase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
2 H2 + ferricytochrome c3 = 4 H+ + ferrocytochrome c3
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
oxidation
-
-
-
-
redox reaction
-
-
-
-
reduction
-
-
-
-
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.
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
cytochrome c3 hydrogenase
-
-
-
-
cytochrome c3 reductase
-
-
-
-
cytochrome hydrogenase
-
-
-
-
Fe-only hydrogenase
-
-
H2:ferricytochrome c3 oxidoreductase
-
-
-
-
hyd B
Desulfovibrio desulfuricans subsp. desulfuricans G20
-
-
-
hydrogenase
-
-
-
-
hydrogenase, cytochrome
-
-
-
-
HysAB
Desulfovibrio vulgaris Hildenborough
-
-
-
[FeFe] hydrogenase
-
-
[FeFe] hydrogenase
Desulfovibrio vulgaris Hildenborough
-
-
-
[Fe] hydrogenase
-
-
[Fe] hydrogenase
Desulfovibrio vulgaris Hildenborough
-
-
-
[Fe]-hydrogenase
-
-
[NiFeSe] Hase
-
-
[NiFeSe] Hase
Desulfovibrio vulgaris Hildenborough
-
-
-
[NiFeSe] hydrogenase
-
-
[NiFeSe] hydrogenase
Desulfovibrio vulgaris Hildenborough
-
;
-
[NiFe] Hase
-
-
[NiFe] Hase
Desulfovibrio vulgaris Hildenborough
-
-
-
[NiFe] hydrogenase 1
Q06173
-
[NiFe]-hydrogenase
-
-
[NiFe]-hydrogenase
-
-
CAS REGISTRY NUMBER
COMMENTARY
9027-05-8
-
9079-91-8
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
Azotobacter chroococcum MCD1
strain MCD1
-
-
Manually annotated by BRENDA team
sulphate reducing bacteria
-
-
Manually annotated by BRENDA team
strain ATCC 7757
-
-
Manually annotated by BRENDA team
strain G20 and cytochrome c3 mutant strain I2
-
-
Manually annotated by BRENDA team
Desulfovibrio desulfuricans ATCC 27774
-
-
-
Manually annotated by BRENDA team
Desulfovibrio desulfuricans Essex
Essex
-
-
Manually annotated by BRENDA team
Desulfovibrio desulfuricans Norway
Norway
-
-
Manually annotated by BRENDA team
Desulfovibrio desulfuricans Norway 4
Norway 4
-
-
Manually annotated by BRENDA team
Desulfovibrio desulfuricans subsp. desulfuricans G20
strain G20
-
-
Manually annotated by BRENDA team
Hildenborough; strain Hildenborough
-
-
Manually annotated by BRENDA team
strain Miyazaki
-
-
Manually annotated by BRENDA team
strain Miyazaki F
-
-
Manually annotated by BRENDA team
Desulfovibrio vulgaris Hildenborough
-
-
-
Manually annotated by BRENDA team
Desulfovibrio vulgaris Hildenborough
Hildenborough
-
-
Manually annotated by BRENDA team
Desulfovibrio vulgaris Hildenborough
Hildenborough; strain Hildenborough
-
-
Manually annotated by BRENDA team
Desulfovibrio vulgaris Hildenborough
strain Hildenborough
-
-
Manually annotated by BRENDA team
Desulfovibrio vulgaris Miyazaki
Miyazaki
-
-
Manually annotated by BRENDA team
Desulfovibrio vulgaris Miyazaki
strain Miyazaki
-
-
Manually annotated by BRENDA team
Desulfovibrio vulgaris Miyazaki F
strain Miyazaki F
-
-
Manually annotated by BRENDA team
strain MR-1
-
-
Manually annotated by BRENDA team
Thiocapsa roseopersicina Bbs
Bbs
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
malfunction
-
the hyd B mutant grows more slowly than the parental strain
malfunction
-
Hyn mutant impairs syntrophic growth but has little effect on growth via sulfate respiration. Cocultures established with DETLAhyd and DELTAhyn-1 mutants achieve cell densities comparable to those of the wild-type on both lactate and pyruvate, but the growth rates are reduced
malfunction
Desulfovibrio desulfuricans subsp. desulfuricans G20
-
the hyd B mutant grows more slowly than the parental strain
-
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
Fe(III)-nitrilotriacetate + ferricytochrome c3
reduced Fe(III)-nitrilotriacetate + ferrocytochrome c3
show the reaction diagram
Desulfovibrio vulgaris, Desulfovibrio vulgaris Hildenborough
-
-
-
-
?
ferricytochrome c3 + 2 H2
ferrocytochrome c3 + 4 H+
show the reaction diagram
-
48% relative activity compared to activity with oxidized methyl viologen
-
-
?
H+ + ferrocytochrome c3
H2 + ferricytochrome c3
show the reaction diagram
-
-
-
-
?
H+ + ferrocytochrome c3
H2 + ferricytochrome c3
show the reaction diagram
Desulfovibrio vulgaris Hildenborough
-
-
-
-
?
H+ + neutral red
H2 + oxidized neutral red
show the reaction diagram
Desulfovibrio desulfuricans, Desulfovibrio desulfuricans Norway
-
-
-
-
?
H+ + phenosafranine
H2 + oxidized phenosafranine
show the reaction diagram
-
-
-
-
?
H+ + reduced methyl viologen
H2 + methyl viologen
show the reaction diagram
-
-
-
-
-
H+ + reduced methyl viologen
H2 + methyl viologen
show the reaction diagram
-
-
-
-
?
H+ + reduced methyl viologen
H2 + methyl viologen
show the reaction diagram
-
weak activity in H2-uptake assay
-
-
r
H+ + reduced methyl viologen
H2 + methyl viologen
show the reaction diagram
Desulfovibrio vulgaris Hildenborough
-
-
-
-
?
H+ + reduced methyl viologen
H2 + methyl viologen
show the reaction diagram
Desulfovibrio vulgaris Miyazaki
-
-
-
-
?
H2 + acceptor
H+ + reduced acceptor
show the reaction diagram
Q06173
electrode-grown cells overexpress the hyn-1 gene for [NiFe] hydrogenase 1
-
-
?
H2 + ammonium pertechnetate
?
show the reaction diagram
-
the reaction requires the presence of c-type cytochromes
-
-
?
H2 + benzyl viologen
H+ + reduced benzyl viologen
show the reaction diagram
Desulfovibrio desulfuricans, Desulfovibrio desulfuricans Norway
-
-
-
r
H2 + ferredoxin
H+ + reduced ferredoxin
show the reaction diagram
-
requires the presence of cytochrome c3 for the reduction of ferredoxin
-
-
?
H2 + ferricytochrome c
H+ + ferrocytochrome c
show the reaction diagram
-
-
-
-
-
H2 + ferricytochrome c
H+ + ferrocytochrome c
show the reaction diagram
-
-
-
-
?
H2 + ferricytochrome c
H+ + ferrocytochrome c
show the reaction diagram
Desulfovibrio desulfuricans, Desulfovibrio desulfuricans Essex
-
nonaheme cytochrome c
-
-
?
H2 + ferricytochrome c
H+ + ferrocytochrome c
show the reaction diagram
Desulfovibrio vulgaris Miyazaki F
-
-
-
-
-
H2 + ferricytochrome c
H+ + ferrocytochrome c
show the reaction diagram
Desulfovibrio vulgaris Hildenborough
-
-
-
-
?
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
-
-
-
-
-
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
-
-
-
-
?
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
-
-
-
-
r
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
-
-
-
-
?
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
-
-
-
-
?
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
-
-
-
-
r
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
-
-
-
-
-
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
-
-
-
-
-
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
-
-
-
-
-
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
-
tetraheme cytochrome c3
-
-
?
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
-
part of an electron transport chain that mediates electronic coupling between periplasmic hydrogen oxidation and cytosolic sulfate reduction, 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
show the reaction diagram
-
the type I cytochrome C3 complex is more efficient than type II cytochrome c3 complex as electron acceptor from hydrogenase
-
-
?
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
-
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
-
-
?
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
-
cytochrome c3 receives two protons and two electrons from hydrogenase for transport to the membrane, and converting electronic energy into proton motive force
-
-
?
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
-
isoform type I cytochrome c3 has the potential to transfer two electrons at a time. The two isoforms type I and type II cytochrome c3 are physiological partners but only single-electron transfers occur in solution
-
-
?
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
Desulfovibrio desulfuricans ATCC 27774
-
cytochrome c3 receives two protons and two electrons from hydrogenase for transport to the membrane, and converting electronic energy into proton motive force
-
-
?
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
Thiocapsa roseopersicina Bbs
-
-
-
-
-
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
Desulfovibrio desulfuricans Norway 4
-
-
-
-
?
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
Desulfovibrio desulfuricans Essex
-
tetraheme cytochrome c3
-
-
?
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
Desulfovibrio vulgaris Miyazaki F
-
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
-
-
?
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
Desulfovibrio vulgaris Hildenborough
-
-
-
-
?
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
Desulfovibrio vulgaris Hildenborough
-
part of an electron transport chain that mediates electronic coupling between periplasmic hydrogen oxidation and cytosolic sulfate reduction, 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
show the reaction diagram
Desulfovibrio vulgaris Hildenborough
-
-
-
-
?
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
Desulfovibrio desulfuricans Norway
-
-
-
-
r
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
Desulfovibrio vulgaris Miyazaki
-
-
-
-
?
H2 + ferricytochrome Hmc
H+ + ferrocytochrome Hmc
show the reaction diagram
Desulfovibrio vulgaris, Desulfovibrio vulgaris Hildenborough
-
13 kDa tetraheme cytochrome c3 forms a complex with a hexadecaheme high molecular weight cytochrome c, i.e. Hmc
-
-
r
H2 + methyl viologen
H+ + reduced methyl viologen
show the reaction diagram
-
-
-
-
?
H2 + methylene blue
H+ + reduced methylene blue
show the reaction diagram
-
-
-
-
?
H2 + methylene blue
H+ + reduced methylene blue
show the reaction diagram
-
no activity in H2-evolution assay
-
-
ir
H2 + methylene blue
H+ + reduced methylene blue
show the reaction diagram
Azotobacter chroococcum, Azotobacter chroococcum MCD1
-
the reation is dependent on the presence of b-type cytochrome HupZ
-
-
r
H2 + methylene blue
H+ + reduced methylene blue
show the reaction diagram
Desulfovibrio desulfuricans Essex
-
-
-
-
?
H2 + methylene blue
H+ + reduced methylene blue
show the reaction diagram
Desulfovibrio desulfuricans Norway
-
no activity in H2-evolution assay
-
-
ir
H2 + oxidized acceptor
H+ + reduced acceptor
show the reaction diagram
Desulfovibrio desulfuricans subsp. desulfuricans, Desulfovibrio desulfuricans subsp. desulfuricans G20
-
-
-
-
?
H2 + oxidized dichloroindophenol
H+ + ?
show the reaction diagram
-
30% relative activity compared to activity with oxidized methyl viologen
-
-
?
H2 + oxidized methyl viologen
H+ + reduced methyl viologen
show the reaction diagram
-
100% relative activity
-
-
?
H2 + potassium ferricyanide
H+ + ?
show the reaction diagram
-
34% relative activity compared to activity with oxidized methyl viologen
-
-
?
H2 + rubredoxin
H+ + reduced rubredoxin
show the reaction diagram
-
requires the presence of cytochrome c3 for the reduction of rubredoxin
-
-
?
lactate + ammonium pertechnetate
?
show the reaction diagram
-
the reaction requires the presence of c-type cytochromes
-
-
?
pyruvate + ferrocytochrome c3
lactate + ferricytochrome c3
show the reaction diagram
-
-
-
-
?
reduced methyl viologen + H+
oxidized methyl viologen + H2
show the reaction diagram
Desulfovibrio vulgaris, Desulfovibrio vulgaris Hildenborough
-
-
-
-
?
lactate + ferrocytochrome c3
pyruvate + ferricytochrome c3
show the reaction diagram
-
-
-
-
?
additional information
?
-
-
enzyme catalyzes production of H2 from Na2S2O4 in presence of cytochrome c3, enzyme can catalyze H-2H exchange in absence of added electron carriers
-
-
-
additional information
?
-
-
enzyme also exhibits high Tc(VII)-reducing activity
-
-
-
additional information
?
-
-
no reduction of ferredoxin, methylene blue or hexacyanoferrate(II) by H2
-
-
-
additional information
?
-
-
a natural electron donor is a low-potential c3 cytochrome
-
-
-
additional information
?
-
-
cytochrome c3 is the natural electron acceptor
-
-
-
additional information
?
-
-
cytochrome c3 is the natural electron acceptor
-
-
-
additional information
?
-
-
cytochrome c3 is the natural electron acceptor
-
-
-
additional information
?
-
-
nonaheme cytochrome c is a competent physiological electron acceptor for the [Ni,Fe] hydrogenase
-
-
-
additional information
?
-
-
cytochrome c3 from Desulfovibrio vulgaris strain Hildenborough, enzyme forms an electron-transfer complex with cytochrome c3 for an electron shuttle between the periplasmic enzyme and the membrane-bound cytochrome c3
-
-
-
additional information
?
-
-
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
-
-
-
additional information
?
-
-
the enzyme is associated to cytochrome c3, a tetraheme 13 kDa metalloprotein, analysis of electron binding, cooperativity effects, the Redox-Bohr effect, and thermodynamics of cytochrome c3
-
-
-
additional information
?
-
-
the enzyme catalyzes the conversion of para-H2 to normal H2 over D2O as well as the isotope exchange reaction in the H2D2O system
-
-
-
additional information
?
-
-
hydrogen-dependent platinum (IV) reducing activity in the presence of hydrogenase and its physiological electron carrier, cytochrome c3
-
-
-
additional information
?
-
Thiocapsa roseopersicina Bbs
-
a natural electron donor is a low-potential c3 cytochrome
-
-
-
additional information
?
-
Desulfovibrio desulfuricans Essex
-
nonaheme cytochrome c is a competent physiological electron acceptor for the [Ni,Fe] hydrogenase
-
-
-
additional information
?
-
Desulfovibrio vulgaris Hildenborough
-
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
-
-
-
additional information
?
-
Desulfovibrio desulfuricans Norway
-
cytochrome c3 is the natural electron acceptor
-
-
-
additional information
?
-
Desulfovibrio vulgaris Miyazaki
-
the enzyme catalyzes the conversion of para-H2 to normal H2 over D2O as well as the isotope exchange reaction in the H2D2O system
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
-
-
-
-
?
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
-
part of an electron transport chain that mediates electronic coupling between periplasmic hydrogen oxidation and cytosolic sulfate reduction
-
-
r
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
-
the type I cytochrome C3 complex is more efficient than type II cytochrome c3 complex as electron acceptor from hydrogenase
-
-
?
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
Desulfovibrio vulgaris Hildenborough
-
part of an electron transport chain that mediates electronic coupling between periplasmic hydrogen oxidation and cytosolic sulfate reduction
-
-
r
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
Desulfovibrio vulgaris Hildenborough
-
-
-
-
?
additional information
?
-
-
a natural electron donor is a low-potential c3 cytochrome
-
-
-
additional information
?
-
-
cytochrome c3 is the natural electron acceptor
-
-
-
additional information
?
-
-
cytochrome c3 is the natural electron acceptor
-
-
-
additional information
?
-
-
cytochrome c3 is the natural electron acceptor
-
-
-
additional information
?
-
-
nonaheme cytochrome c is a competent physiological electron acceptor for the [Ni,Fe] hydrogenase
-
-
-
additional information
?
-
Thiocapsa roseopersicina Bbs
-
a natural electron donor is a low-potential c3 cytochrome
-
-
-
additional information
?
-
Desulfovibrio desulfuricans Essex
-
nonaheme cytochrome c is a competent physiological electron acceptor for the [Ni,Fe] hydrogenase
-
-
-
additional information
?
-
Desulfovibrio desulfuricans Norway
-
cytochrome c3 is the natural electron acceptor
-
-
-
COFACTOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
cytochrome c
-
nonaheme cytochrome c is a competent physiological electron acceptor
cytochrome c3
-
requires the presence of cytochrome c3 for the reduction of ferredoxin, rubredoxin and cytochrome c3
-
cytochrome c3
-
-
-
cytochrome c3
-
tetraheme cytochrome c3
-
cytochrome c3
-
-
-
cytochrome c3
-
-
-
cytochrome c3
-
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
-
cytochrome c3
-
-
-
cytochrome c3
-
the enzyme is associated to cytochrome c3, a tetraheme 13 kDa metalloprotein, analysis of electron binding, cooperativity effects, the Redox-Bohr effect, and thermodynamics of cytochrome c3
-
cytochrome c3
-
hydrogen-dependent platinum (IV) reducing activity in the presence of hydrogenase and its physiological electron carrier, cytochrome c3. Reduction of platinum by the purified hydrogenase enzyme alone yields about 10% removal after 3 h incubation while after the addition of cytochrome c3 there is a slight increase to 15%. Suppression of enzyme activity due to the extreme acid pH of 0.38 of the effluent
-
heme
-
contains 4 heme per mol
iron-sulfur centre
-
the active site of this protein is located in the large subunit, and the small subunit contains one [3Fe4S] and two [4Fe4S] iron-sulfur centres
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Fe
-
NiFeSe enzyme; [NiFeSe] enzyme, ratio Ni:Se:Fe is 1:1:15
Fe2+
-
4 Fe2+ per mol of enzyme
Iron
-
presence of a three-iron center
Iron
-
11-12 gatom of nonheme iron per molecule; nonheme iron protein
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
Iron
-
contains 6 iron atoms and six acid-labile sulfur groups per molecule, presence of [4Fe-4S]3+ or [3Fe-3S]3+
Iron
-
iron-sulfur protein, 7-9 iron atoms and 7-8 labile sulfide ions
Iron
-
4.8 iron atoms per molecule
Iron
-
[Ni,Fe] hydrogenase
Iron
-
4Fe-4S clusters
Iron
-
[NiFeSe] hydrogenase
Iron
-
[Ni,Fe] hydrogenase
Iron
-
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
-
increases activity by 1.8%
Ni
-
NiFeSe enzyme, contains selenium in equimolar amounts to Ni; [NiFeSe] enzyme, ratio Ni:Se:Fe is 1:1:15
Ni2+
-
1 Ni2+ per mol of enzyme
Nickel
-
1 gatom of nickel per molecule
Nickel
-
purified enzyme contains variable amounts of nickel, ranging from 0.1 to 0.6 gatom per mol of enzyme
Nickel
-
0.45 nickel atoms per molecule
Nickel
-
[Ni,Fe] hydrogenase
Nickel
-
[NiFeSe] hydrogenase
Nickel
-
[Ni,Fe] hydrogenase
Nickel
-
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
-
increases activity by 1.6%
Se
-
NiFeSe enzyme, contains selenium in equimolar amounts to Ni; [NiFeSe] enzyme, ratio Ni:Se:Fe is 1:1:15
selenium
-
0.45 selenium atoms per molecule
selenium
-
[NiFeSe] hydrogenase
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
Ag+
-
1 mM, 97% inhibition
Cr6+
-
1 mM, complete inhibition
Cu2+
-
1 mM, 95% inhibition
dimethyl sulfoxide
-
-
EDTA
-
10 mM, 10% inhibition
KI
-
above 0.5 M, considerable inhibition of H2 evolution
N-bromosuccinimide
-
0.07 mM, complete loss of activity
NaCl
-
above 0.5 M, considerable inhibition of H2 evolution
NaF
-
above 0.5 M, considerable inhibition of H2 evolution
NEM
-
2 mM; 60% inhibition
O2
-
reversible inactivation
O2
-
strong inhibition of H2 evolution from reduced methyl viologen
O2
P18187
wild-type tends to attract O2 molecules close to the active site
p-chloromercuribenzene sulfonate
-
1 mM; 87% inhibition
PCMB
-
0.17 mM, 35% inhibition
SDS
-
0.1%, 86-99% inactivation
Zn2+
-
1 mM, 79% inhibition
ACTIVATING COMPOUND
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
Phospholipid
-
H2-production from reduced methyl viologen requires phospholipids
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.025
-
cytochrome c
-
nonaheme cytochrome c
0.0126
-
cytochrome c3
-
tetraheme cytochrome c3
-
0.0026
-
ferricytochrome c
-
25C, pH 7.0, wild-type cytochrome c3
0.0368
-
ferricytochrome c3
-
-
-
0.002
-
ferrocytochrome c3
-
H2-evolution assay
-
0.075
-
ferrocytochrome c3
-
H2-evolution reaction
-
0.0099
-
mutant cytochrome c K101M
-
25C, pH 7.0, mutant cytochrome c3 K101M
-
0.0027
-
mutant cytochrome c K10M
-
25C, pH 7.0, mutant cytochrome c3 K10M
-
0.0045
-
mutant cytochrome c K15M
-
25C, pH 7.0, mutant cytochrome c3 K15M
-
0.003
-
mutant cytochrome c K26M
-
25C, pH 7.0, mutant cytochrome c3 K26M
-
0.0051
-
mutant cytochrome c K57M
-
25C, pH 7.0, mutant cytochrome c3 K57M
-
0.0057
-
mutant cytochrome c K58M
-
25C, pH 7.0, mutant cytochrome c3 K58M
-
0.0104
-
mutant cytochrome c K60M
-
25C, pH 7.0, mutant cytochrome c3 K60M
-
0.0067
-
mutant cytochrome c K72M
-
25C, pH 7.0, mutant cytochrome c3 K72M
-
0.0057
-
mutant cytochrome c K94M
-
25C, pH 7.0, mutant cytochrome c3 K94M
-
0.0073
-
mutant cytochrome c K95M
-
25C, pH 7.0, mutant cytochrome c3 K95M
-
0.0022
-
mutant cytochrome c Y65A
-
25C, pH 7.0, mutant cytochrome c3 Y65A
-
0.0043
-
mutant cytochrome c Y66L
-
25C, pH 7.0, mutant cytochrome c3 Y66L
-
0.08
-
reduced benzyl viologen
-
H2-evolution assay
0.003
-
reduced methyl viologen
-
H2-evolution assay
0.032
-
[Fe] hydrogenase-cytochrome c3 complex
-
pH 7.0, electron transfer kinetics
-
0.006
-
[Fe] hydrogenase-cytochrome c3-cytochrome Hmc complex
-
pH 7.0, electron transfer kinetics
-
0.04
-
[Fe] hydrogenase-cytochrome Hmc complex
-
pH 7.0, electron transfer kinetics
-
0.0052
-
methyl viologen
-
-
additional information
-
additional information
-
kinetic studies of hydrogenase in sodium di-2-ethylhexylsulfosuccinate reversed micelles
-
additional information
-
additional information
-
kinetic properties of the enzyme
-
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
-
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
49
-
ferricytochrome c
-
25C, pH 7.0, wild-type cytochrome c3
38
-
ferricytochrome c3
-
-
-
490
-
ferricytochrome c3
-
-
-
51
-
mutant cytochrome c K101M
-
25C, pH 7.0
-
45
-
mutant cytochrome c K15M
-
25C, pH 7.0
-
44
-
mutant cytochrome c K26M
-
25C, pH 7.0
-
48
-
mutant cytochrome c K57M
-
25C, pH 7.0
-
45
-
mutant cytochrome c K58M
-
25C, pH 7.0
-
46
-
mutant cytochrome c K60M
-
25C, pH 7.0
-
42
-
mutant cytochrome c K72M
-
25C, pH 7.0
-
45
-
mutant cytochrome c K94M, mutant cytochrome c K95M
-
25C, pH 7.0
-
49
-
mutant cytochrome c Y65A
-
25C, pH 7.0
-
47
-
mutant cytochrome c Y66L
-
25C, pH 7.0
-
48
-
mutant cytochrome c3 K10M
-
25C, pH 7.0
-
462
-
[Fe] hydrogenase-cytochrome c3 complex
-
pH 7.0, electron transfer kinetics
-
2.3
-
[Fe] hydrogenase-cytochrome c3-cytochrome Hmc complex
-
pH 7.0, electron transfer kinetics
-
0.15
-
[Fe] hydrogenase-cytochrome Hmc complex
-
pH 7.0, electron transfer kinetics
-
3.6
-
methyl viologen
-
-
additional information
-
additional information
-
-
-
Ki VALUE [mM]
Ki VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
additional information
-
additional information
-
Ki for CO is 1.64 kPa
-
additional information
-
additional information
-
Ki for CO is 8.9 Torr
-
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
3817
-
-
crude sonicate
35340
-
-
9.26fold purified
additional information
-
-
wild-type and cytochrome c3 mutant strains: reduction rates of uranium(VI) with different electron donors lactate, pyruvate, and hydrogen via essential cytochrome c3
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
5
6
-
cytochrome c3-dependent H2 evolution
6
7
-
methyl viologen-dependent H2 evolution
6
8
-
H-2H exchange
6
-
-
H2 production
6.5
-
-
H2-evolution assay
7.5
8
-
-
8
9
-
cytochrome c3 reduction by H2
pH RANGE
pH RANGE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
5
9
-
pH 5.0: about 30% of maximal activity, pH 9.0: about 35% of maximal activity
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
35
40
-
-
SOURCE TISSUE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE
Desulfovibrio vulgaris Hildenborough
-
-
-
Manually annotated by BRENDA team
additional information
-
uranyl acetate or uranyl nitrate as sole electron acceptor is not sufficient for cell growth and is growth-inhibitory at higher concentrations
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
Thiocapsa roseopersicina Bbs
-
-
-
Manually annotated by BRENDA team
-
; 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)
-
Manually annotated by BRENDA team
Desulfovibrio vulgaris Hildenborough
-
; 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)
-
-
Manually annotated by BRENDA team
Desulfovibrio desulfuricans Norway
-
bound to
-
Manually annotated by BRENDA team
Desulfovibrio desulfuricans Norway 4
-
bound to; bound to
-
Manually annotated by BRENDA team
Desulfovibrio vulgaris Hildenborough, Thiocapsa roseopersicina Bbs
-
-
-
Manually annotated by BRENDA team
Desulfovibrio vulgaris Miyazaki
-
-
-
-
Manually annotated by BRENDA team
Desulfovibrio desulfuricans Essex, Desulfovibrio desulfuricans Norway 4
-
-
-
-
Manually annotated by BRENDA team
Desulfovibrio vulgaris Hildenborough
-
;
-
-
Manually annotated by BRENDA team
-
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)
-
Manually annotated by BRENDA team
Azotobacter chroococcum MCD1, Desulfovibrio desulfuricans Norway 4
-
-
-
-
Manually annotated by BRENDA team
Desulfovibrio vulgaris Hildenborough
-
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)
-
-
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
Desulfovibrio fructosivorans
Desulfovibrio fructosivorans
Desulfovibrio fructosivorans
Desulfovibrio fructosivorans
Desulfovibrio fructosivorans
Desulfovibrio fructosivorans
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
13000
-
-
cytochrome c3
58000
-
-
gel filtration
60000
-
-
gel filtration
61000
-
-
membrane-bound enzyme, gel filtration
67000
-
-
soluble enzyme, gel filtration
76000
-
-
gel filtration
88000
-
-
SDS-PAGE
89000
-
-
low-speed equilibrium sedimentation
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
?
-
x * 26000 + x * 62000
?
-
x * 63000 + x * 35000, SDS-PAGE
?
-
x * 58000, SDS-PAGE
?
Desulfovibrio vulgaris Hildenborough
-
x * 63000 + x * 35000, SDS-PAGE
-
dimer
-
1 * 28000 + 1 * 59000, SDS-PAGE
dimer
-
1 * 27100 + 1 * 59800, membrane-bound enzyme, SDS-PAGE; 1 * 28600 + 1 * 56400, soluble enzyme, SDS-PAGE
dimer
-
1 * 25000 + 1 * 47000
dimer
Desulfovibrio desulfuricans Norway 4
-
1 * 27100 + 1 * 59800, membrane-bound enzyme, SDS-PAGE; 1 * 28600 + 1 * 56400, soluble enzyme, SDS-PAGE
-
dimer
Desulfovibrio vulgaris Miyazaki
-
1 * 28000 + 1 * 59000, SDS-PAGE
-
dimer
Thiocapsa roseopersicina Bbs
-
1 * 25000 + 1 * 47000
-
heterodimer
-
1 * 62000 + 1 * 26000, SDS-PAGE
monomer
-
1 * 58000, SDS-PAGE
monomer
Desulfovibrio desulfuricans Norway
-
1 * 58000, SDS-PAGE
-
additional information
-
2 protein bands detected by SDS-PAGE, 30500 Da and 62000 Da, cytochrome c3 has a MW of 14000 Da, determined by SDS-PAGE
additional information
-
NMR study, structural model of the electron-transfer complex formed by enzyme and cytochrome c3, the latter with MW of 13 kDa containing 4 hemes which are associated to the distal cluster of the enzyme involving lysine residues K15, K57, K58, K60, K72, K94, K95, and K101, overview
additional information
-
the enzyme is associated to cytochrome c3, a tetraheme 13 kDa metalloprotein, structure analysis, modeling study
additional information
Desulfovibrio desulfuricans Essex
-
2 protein bands detected by SDS-PAGE, 30500 Da and 62000 Da, cytochrome c3 has a MW of 14000 Da, determined by SDS-PAGE
-
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
lipoprotein
-
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
lipoprotein
-
-
lipoprotein
Desulfovibrio vulgaris Hildenborough
-
; 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 ACCESSION NO.
LITERATURE
X-ray diffraction structure determination and analysis of purified reduced cytochrome C3, which is associated with the enzyme, at 0.1 M Tris-HCl, pH 7.6, and 60% PEG 400, at 1.35-1.4 A resolution, comparison to the structure of oxidized cytochrome c3 at pH 4.0, overview, modeling
-
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
-
TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
4
-
-
4 weeks, atmosphere of N2, air or H2, very little loss of activity
23
-
-
atmosphere of N2, air or H2, 40% loss of activity after 2 weeks, complete loss of activity after 4 weeks
35
40
-
at optimal temperature range of 35-40C, a minimal activity loss during the first 10 to 20 min and thereafter, activity steadily decreases as incubation time increases. After 80 min of incubation, the enzyme loses 75-80% of all of its activity
50
-
-
10 min, H2 evolution in presence of methyl viologen, no decrease in activity
55
-
-
completely denatured above
60
-
-
10 min, H2 evolution in presence of methyl viologen, 30% loss of activity
70
-
-
10 min, H2 evolution in presence of methyl viologen, 37% loss of activity
77
-
-
stable below, 2 h
80
-
-
10 min, H2 evolution in presence of methyl viologen, 69% loss of activity
80
-
-
stable below
90
-
-
10 min, H2 evolution in presence of methyl viologen, 99% loss of activity
100
-
-
10 min, H2 evolution in presence of methyl viologen, complete loss of activity
GENERAL STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
operational stability of enzyme encapsulated in sodium dioctylsulfosuccinate reversed micelles and dependence of stability on the water content, enzyme concentration, pH, temperature and organic solvents, deactivation is strongly dependent on the cohesion of the micellar aggregates containing the enzyme
-
sodium di-2-ethylhexylsulfosuccinate seems to denaturate the enzyme
-
ORGANIC SOLVENT
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
dodecane
-
t1/2: 2.9 h
hexane
-
t1/2: 13.1 h
isooctane
-
t1/2: 9.5 h
urea
-
9 M, 24 h, room temperature, stable
urea
Desulfovibrio vulgaris Miyazaki
-
9 M, 24 h, room temperature, stable
-
OXIDATION STABILITY
ORGANISM
UNIPROT ACCESSION NO.
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
resistance of the [NiFeSe] Hase to inactivation by oxygen
-
674919
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
4C, atmosphere of N2, air or H2, very little loss of activity after 4 weeks
-
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
by sonication, PEG 20000 concentration, ion exchange chromatography and gel filtration, 9.26fold purified with a yield of 51.8%
-
membrane-bound enzyme
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
ligated into plasmid pMO719 and expressed in Escherichia coli GC5 competent cells
-
EXPRESSION
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
during syntrophic growth on lactate with a hydrogenotrophic methanogen, Hyn is upregulated compared with its expression in sulfate-limited monocultures
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
additional information
-
a cytochrome c3 mutant strain I2 is impaired in reduction of uranium(VI) utilizing electrons from donors lactate, pyruvate or hydrogen transferred via cytochrome c3, the strongest effect is senn with hydrogen as electron donor
V74Q
P18187
while wild-type tends to attract O2 molecules close to the active site, the V74Q mutant favors the localization of O2 about 20 A away from it. In the mutant, the glutamine residue produces an energy barrier height higher than the one found when a valine is present as in wild-type. In the V74Q mutant, the enzyme inhibition by O2 is lowered from both a kinetic and a thermodynamic point of view with respect to the wild-type enzyme
additional information
-
Hyn mutant impairs syntrophic growth but has little effect on growth via sulfate respiration. Cocultures established with DETLAhyd and DELTAhyn-1 mutants achieve cell densities comparable to those of the wild-type on both lactate and pyruvate, but the growth rates are reduced
APPLICATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
industry
-
platinum (IV) recovery from an industrial effluent through a biosulphidogenic sulphate reducing bacteria consortium via a hydrogenase-cytochrome c3 enzyme system that removes electrons from hydrogen to the platinum metal that acts as a final electron acceptor
environmental protection
-
enzyme might be useful in development of a mechanism to remove contaminating uranium from groundwaters
synthesis
-
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
environmental protection
Desulfovibrio vulgaris Hildenborough
-
enzyme might be useful in development of a mechanism to remove contaminating uranium from groundwaters
-
synthesis
Desulfovibrio vulgaris Hildenborough
-
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
-