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 hide
1.12.2.1
-
RECOMMENDED NAME
GeneOntology No.
cytochrome-c3 hydrogenase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
2 H2 + ferricytochrome c3 = 4 H+ + ferrocytochrome c3
show the reaction diagram
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-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
-
-
-
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redox reaction
-
-
-
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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.
CAS REGISTRY NUMBER
COMMENTARY hide
9027-05-8
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9079-91-8
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain MCD1
-
-
Manually annotated by BRENDA team
strain MCD1
-
-
Manually annotated by BRENDA team
sulphate reducing bacteria
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Essex
-
-
Manually annotated by BRENDA team
Norway
-
-
Manually annotated by BRENDA team
Desulfovibrio desulfuricans Norway 4
Norway 4
-
-
Manually annotated by BRENDA team
Desulfovibrio vulgaris Miyazaki F
strain Miyazaki F
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
strain MR-1
-
-
Manually annotated by BRENDA team
Bbs
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-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
Fe(III)-nitrilotriacetate + ferricytochrome c3
reduced Fe(III)-nitrilotriacetate + ferrocytochrome c3
show the reaction diagram
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+ + neutral red
H2 + oxidized neutral red
show the reaction diagram
H+ + phenosafranine
H2 + oxidized phenosafranine
show the reaction diagram
-
-
-
-
?
H+ + reduced methyl viologen
H2 + methyl viologen
show the reaction diagram
H2 + acceptor
H+ + reduced acceptor
show the reaction diagram
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
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 c3
H+ + ferrocytochrome c3
show the reaction diagram
H2 + ferricytochrome Hmc
H+ + ferrocytochrome Hmc
show the reaction diagram
H2 + methyl viologen
H+ + reduced methyl viologen
show the reaction diagram
-
-
-
-
?
H2 + methylene blue
H+ + reduced methylene blue
show the reaction diagram
H2 + oxidized acceptor
H+ + reduced acceptor
show the reaction diagram
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
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34% relative activity compared to activity with oxidized methyl viologen
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-
?
H2 + rubredoxin
H+ + reduced rubredoxin
show the reaction diagram
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requires the presence of cytochrome c3 for the reduction of rubredoxin
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-
?
lactate + ammonium pertechnetate
?
show the reaction diagram
-
the reaction requires the presence of c-type cytochromes
-
-
?
lactate + ferrocytochrome c3
pyruvate + ferricytochrome c3
show the reaction diagram
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-
-
-
?
pyruvate + ferrocytochrome c3
lactate + ferricytochrome c3
show the reaction diagram
-
-
-
-
?
reduced methyl viologen + H+
oxidized methyl viologen + H2
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
H2 + ferricytochrome c3
H+ + ferrocytochrome c3
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
cytochrome c
-
nonaheme cytochrome c is a competent physiological electron acceptor
cytochrome c3
iron-sulfur centre
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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
COMMENTARY hide
LITERATURE
Fe2+
-
4 Fe2+ per mol of enzyme
Ni2+
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1 Ni2+ per mol of enzyme
Se
-
NiFeSe enzyme, contains selenium in equimolar amounts to Ni; [NiFeSe] enzyme, ratio Ni:Se:Fe is 1:1:15
selenium
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Ag+
-
1 mM, 97% inhibition
Cr6+
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1 mM, complete inhibition
Cu2+
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1 mM, 95% inhibition
dimethyl sulfoxide
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-
EDTA
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10 mM, 10% inhibition
KI
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above 0.5 M, considerable inhibition of H2 evolution
N-bromosuccinimide
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0.07 mM, complete loss of activity
NaCl
-
above 0.5 M, considerable inhibition of H2 evolution
NaF
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above 0.5 M, considerable inhibition of H2 evolution
NEM
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2 mM; 60% inhibition
p-chloromercuribenzene sulfonate
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1 mM; 87% inhibition
PCMB
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0.17 mM, 35% inhibition
SDS
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0.1%, 86-99% inactivation
Zn2+
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1 mM, 79% inhibition
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Phospholipid
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H2-production from reduced methyl viologen requires phospholipids
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.025
cytochrome c
-
nonaheme cytochrome c
0.0126
cytochrome c3
-
tetraheme cytochrome c3
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0.0026
ferricytochrome c
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25C, pH 7.0, wild-type cytochrome c3
0.0368
ferricytochrome c3
-
-
0.002 - 0.075
ferrocytochrome c3
0.0052
methyl viologen
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-
0.0099
mutant cytochrome c K101M
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25C, pH 7.0, mutant cytochrome c3 K101M
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0.0027
mutant cytochrome c K10M
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25C, pH 7.0, mutant cytochrome c3 K10M
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0.0045
mutant cytochrome c K15M
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25C, pH 7.0, mutant cytochrome c3 K15M
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0.003
mutant cytochrome c K26M
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25C, pH 7.0, mutant cytochrome c3 K26M
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0.0051
mutant cytochrome c K57M
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25C, pH 7.0, mutant cytochrome c3 K57M
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0.0057
mutant cytochrome c K58M
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25C, pH 7.0, mutant cytochrome c3 K58M
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0.0104
mutant cytochrome c K60M
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25C, pH 7.0, mutant cytochrome c3 K60M
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0.0067
mutant cytochrome c K72M
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25C, pH 7.0, mutant cytochrome c3 K72M
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0.0057
mutant cytochrome c K94M
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25C, pH 7.0, mutant cytochrome c3 K94M
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0.0073
mutant cytochrome c K95M
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25C, pH 7.0, mutant cytochrome c3 K95M
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0.0022
mutant cytochrome c Y65A
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25C, pH 7.0, mutant cytochrome c3 Y65A
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0.0043
mutant cytochrome c Y66L
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25C, pH 7.0, mutant cytochrome c3 Y66L
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0.08
reduced benzyl viologen
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H2-evolution assay
0.003
reduced methyl viologen
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H2-evolution assay
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
-
additional information
additional information
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
49
ferricytochrome c
Desulfovibrio vulgaris
-
25C, pH 7.0, wild-type cytochrome c3
38 - 490
ferricytochrome c3
3.6
methyl viologen
Bacteria
-
-
51
mutant cytochrome c K101M
Desulfovibrio vulgaris
-
25C, pH 7.0
-
45
mutant cytochrome c K15M
Desulfovibrio vulgaris
-
25C, pH 7.0
-
44
mutant cytochrome c K26M
Desulfovibrio vulgaris
-
25C, pH 7.0
-
48
mutant cytochrome c K57M
Desulfovibrio vulgaris
-
25C, pH 7.0
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45
mutant cytochrome c K58M
Desulfovibrio vulgaris
-
25C, pH 7.0
-
46
mutant cytochrome c K60M
Desulfovibrio vulgaris
-
25C, pH 7.0
-
42
mutant cytochrome c K72M
Desulfovibrio vulgaris
-
25C, pH 7.0
-
45
mutant cytochrome c K94M, mutant cytochrome c K95M
Desulfovibrio vulgaris
-
25C, pH 7.0
-
49
mutant cytochrome c Y65A
Desulfovibrio vulgaris
-
25C, pH 7.0
-
47
mutant cytochrome c Y66L
Desulfovibrio vulgaris
-
25C, pH 7.0
-
48
mutant cytochrome c3 K10M
Desulfovibrio vulgaris
-
25C, pH 7.0
-
462
[Fe] hydrogenase-cytochrome c3 complex
Desulfovibrio vulgaris
-
pH 7.0, electron transfer kinetics
-
2.3
[Fe] hydrogenase-cytochrome c3-cytochrome Hmc complex
Desulfovibrio vulgaris
-
pH 7.0, electron transfer kinetics
-
0.15
[Fe] hydrogenase-cytochrome Hmc complex
Desulfovibrio vulgaris
-
pH 7.0, electron transfer kinetics
-
additional information
additional information
Desulfovibrio desulfuricans
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-
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
additional information
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
3817
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crude sonicate
35340
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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
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 6
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cytochrome c3-dependent H2 evolution
6 - 7
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methyl viologen-dependent H2 evolution
6 - 8
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H-2H exchange
6
-
H2 production
6.5
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H2-evolution assay
7.5 - 8
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-
8 - 9
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cytochrome c3 reduction by H2
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 9
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pH 5.0: about 30% of maximal activity, pH 9.0: about 35% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
35 - 40
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-
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
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
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
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)
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
13000
-
cytochrome c3
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
COMMENTARY hide
LITERATURE
heterodimer
-
1 * 62000 + 1 * 26000, SDS-PAGE
monomer
additional information
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
lipoprotein
Crystallization/COMMENTARY
ORGANISM
UNIPROT
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
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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
ORGANISM
UNIPROT
COMMENTARY hide
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
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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
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
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
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sodium di-2-ethylhexylsulfosuccinate seems to denaturate the enzyme
-
ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dodecane
-
t1/2: 2.9 h
hexane
-
t1/2: 13.1 h
isooctane
-
t1/2: 9.5 h
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
resistance of the [NiFeSe] Hase to inactivation by oxygen
-
674919
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4C, atmosphere of N2, air or H2, very little loss of activity after 4 weeks
-
Purification/COMMENTARY
ORGANISM
UNIPROT
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
LITERATURE
ligated into plasmid pMO719 and expressed in Escherichia coli GC5 competent cells
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
during syntrophic growth on lactate with a hydrogenotrophic methanogen, Hyn is upregulated compared with its expression in sulfate-limited monocultures
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
V74Q
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
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
environmental protection
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
synthesis
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