Information on EC 1.12.7.2 - ferredoxin hydrogenase

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

EC NUMBER
COMMENTARY hide
1.12.7.2
-
RECOMMENDED NAME
GeneOntology No.
ferredoxin hydrogenase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
H2 + 2 oxidized ferredoxin = 2 reduced ferredoxin + 2 H+
show the reaction diagram
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-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
-
-
-
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redox reaction
-
-
-
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reduction
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
carbon monoxide dehydrogenase complex
-
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hydrogen production
-
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hydrogen production III
-
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hydrogen production VI
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hydrogen production VIII
-
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L-glutamate degradation VII (to butanoate)
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superpathway of fermentation (Chlamydomonas reinhardtii)
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SYSTEMATIC NAME
IUBMB Comments
hydrogen:ferredoxin oxidoreductase
Contains iron-sulfur clusters. The enzymes from some sources contains nickel. Can use molecular hydrogen for the reduction of a variety of substances.
CAS REGISTRY NUMBER
COMMENTARY hide
9080-02-8
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
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Manually annotated by BRENDA team
strain ATC 19859
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Manually annotated by BRENDA team
strain ATC 19859
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-
Manually annotated by BRENDA team
strain 137 C(+)
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-
Manually annotated by BRENDA team
Chlorococcum submarinum
-
-
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Manually annotated by BRENDA team
strain MR 505
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Manually annotated by BRENDA team
strain H16, ATCC 17699
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Manually annotated by BRENDA team
strain H16, ATCC 17699
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-
Manually annotated by BRENDA team
Desulfovibrio vulgaris Hildenborough ATCC 29579
strain Hildenborough ATCC 29579
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Manually annotated by BRENDA team
IIT-BT08 (MTCC 5373)
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Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
strain LC1, formerly Peptostreptococcus elsdenii
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Manually annotated by BRENDA team
strain Fusaro DSM 804
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Manually annotated by BRENDA team
strain MS, DSM 800
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Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
strain DSM 2875
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Manually annotated by BRENDA team
strain NCIM 1605
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Manually annotated by BRENDA team
Tetraselmis sp. KSN-2002 NCIM 1605
strain NCIM 1605
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(SeO3)2- + H2 + ?
Se + H2O + ?
show the reaction diagram
(TeO3)2- + H2 + ?
Te + H2O + ?
show the reaction diagram
2 H+ + reduced ferredoxin
H2 + oxidized ferredoxin
show the reaction diagram
2 H+ + reduced polyferredoxin
H2 + oxidized polyferredoxin
show the reaction diagram
H+ + reduced benzyl viologen
H2 + oxidized benzyl viologen
show the reaction diagram
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58.8% relative activity, purified enzyme
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-
?
H+ + reduced ferredoxin
H2 + oxidized ferredoxin
show the reaction diagram
H+ + reduced methyl viologen
H2 + oxidized methyl viologen
show the reaction diagram
H2 + 2 oxidized ferredoxin
2 reduced ferredoxin + 2 H+
show the reaction diagram
Q8U0Z8 and Q8U0Z7 and Q8U0Z6
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-
-
?
H2 + electron acceptor
H+ + reduced electron acceptor
show the reaction diagram
H2 + ferredoxin + oxidized metronidazole
H+ + ferredoxin + reduced metronidazole
show the reaction diagram
H2 + oxidized benzyl viologen
reduced benzyl viologen + H+
show the reaction diagram
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wild-type enzyme catalysed the reduction of benzylviologen at fourfold higher rates than the reduction of ferredoxin
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-
?
H2 + oxidized CAC3527 ferredoxin
H+ + reduced CAC3527 ferredoxin
show the reaction diagram
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mutant CAC3527 ferredoxin displays an almost 8fold lower reduction potential than wild type ferredoxin
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r
H2 + oxidized ferredoxin
H+ + reduced ferredoxin
show the reaction diagram
H2 + oxidized ferredoxin
reduced ferredoxin + 2 H+
show the reaction diagram
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-
-
-
?
H2 + oxidized ferredoxin
reduced ferredoxin + H+
show the reaction diagram
H2 + oxidized ferredoxin CAC0587
H+ + reduced ferredoxin CAC0587
show the reaction diagram
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ferredoxin CAC0587 is the standard major ferredoxin
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-
r
H2 + oxidized flavodoxin CAC0587
H+ + reduced flavodoxin CAC0587
show the reaction diagram
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flavodoxin CAC0587 is the standard major flavodoxin
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r
H2 + oxidized methyl viologen
H+ + reduced methyl viologen
show the reaction diagram
S + NADPH
H2S + NADP+
show the reaction diagram
additional information
?
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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
2 H+ + reduced ferredoxin
H2 + oxidized ferredoxin
show the reaction diagram
-
the exergonic reaction is coupled to energy conservation by means of electron-transport phosphorylation
-
-
?
2 H+ + reduced polyferredoxin
H2 + oxidized polyferredoxin
show the reaction diagram
H+ + reduced ferredoxin
H2 + oxidized ferredoxin
show the reaction diagram
H2 + oxidized ferredoxin
H+ + reduced ferredoxin
show the reaction diagram
H2 + oxidized ferredoxin
reduced ferredoxin + H+
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
FAD
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hydrogenase II, 0.83 mol per mol heterotetramer; putative nucleotide-binding site in the gamma subunit
Ferredoxin
iron-sulfur centre
NADH
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putative nucleotide-binding site in the gamma subunit
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Iron
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one mol of HydA contains 7 mol iron
Ni2+
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contains 1 g atoms of Ni per mole of protein
Se
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the large subunit contains a selenocysteine
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2,2'-bipyridyl
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66% activity at 1 mM
2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone
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inhibition of H2 production, photosystem 1 is involved in the supply of electrons to the hydrogenase
EDTA
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at 0.2 M 35% inhibition of hydrogen production and 27% inhibition of hydrogen oxidation
ethylene glycol
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inhibitory to hydrogen production
guanidine hydrochloride
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at 10 mM inhibitory, hydrogen production
o-phenanthroline
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36% activity at 1 mM
phenylmethanesulfonyl fluoride
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61% activity at 1 mM
Procion red
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competitive inhibition, bidirectional hydrogenase
Sodium mersalyl
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at 12.2 mol per mol protein, 70% inhibition
sulfo-disalicylidinepropandiamine
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hydrogenase activity is reduced up to 30-fold
Tiron
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inhibits methyl viologen hydrogen oxidation
Tris-HCl
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at 30 mM inhibitory, hydrogen production
Urea
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at 10 mM inhibitory, hydrogen production
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
HydEF protein
required for [FeFe]-hydrogenase activity
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HydG protein
required for [FeFe]-hydrogenase activity
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MgCl2
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up to 0.5 M, activation of methyl or benzyl viologen mediated hydrogen oxidation
NaCl
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up to 0.5 M, activation of methyl or benzyl viologen mediated hydrogen oxidation
rubredoxin
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3fold increase of sulfur reductase activity at pH 7.6
Tris-HCl
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at pH 8, activation of methyl or benzyl viologen mediated hydrogen oxidation
additional information
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5 - 5.7
benzyl viologen
0.00068 - 0.13
Ferredoxin
0.000033 - 5.6
H2
0.31 - 171
methyl viologen
0.18 - 0.4
methylene blue
0.125
NAD+
-
-
0.07
NADH
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-
0.017
NADP+
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-
0.07
NADPH
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0.003 - 0.72
reduced ferredoxin
0.57 - 6.25
reduced methyl viologen
0.2
sulfur
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.683 - 483
H2
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.004
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hydrogen oxidation, benzyl viologen as electron acceptor
0.02
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hydrogen production, oxidized ferredoxin as electron donor, hydrogenase II
0.107
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crude extract
0.2
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sulfur reduction, hydrogenase II
0.26
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crude extract
0.69
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hydrogen oxidation, methylene blue as electron acceptor
0.98
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hydrogen production, sodium dithionite as electron donor, hydrogenase II
3.5
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hydrogen production, methyl viologen as electron donor, hydrogenase II
5
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hydrogen evolution
6.02
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hydrogen oxidation, methylene blue as electron acceptor
7.8
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hydrogen oxidation, phenosafranine as electron acceptor
9.4
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hydrogen evolution, reduced methyl viologen as electron donor
19.8
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hydrogen oxidation, benzyl viologen as electron acceptor
28
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recombinant, purified enzyme
38.5
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reduction of metronidiazole
40
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hydrogen production, methyl viologen as electron donor, hydrogenase II
45
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hydrogen production, methyl viologen as electron donor
53
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hydrogen oxidation, methyl viologen as electron acceptor
61
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hydrogen oxidation, methylene blue as electron acceptor, hydrogenase I
75.7
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hydrogen evolution, reduced methyl viologen as electron donor
89
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hydrogen production, methyl viologen as electron donor
90
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hydrogen evolution, ferredoxin as electron donor
94
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hydrogen mediated selenite reduction
96
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hydrogen oxidation, benzyl viologen as electron acceptor
98.6
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hydrogen oxidation, methyl viologen as electron acceptor
120
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hydrogen oxidation, methyl viologen as electron acceptor
121
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hydrogen oxidation
123
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hydrogen oxidation, methylene blue as electron acceptor
131
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hydrogen oxidation, benzyl viologen as electron acceptor, hydrogenase II
174
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hydrogen oxidation, benzyl viologen as electron acceptor
210
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hydrogen oxidation, benzyl viologen as electron acceptor
335
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1284fold purified enzyme
391
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reduction of methyl viologen
400
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hydrogen oxidation, methyl viologen as electron acceptor
510
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reaction with methyl viologen
700
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hydrogen evolution
935
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hydrogen production, reduced methyl viologen as electron donor
1260
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oxidation of methyl viologen
1470
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after addition of 1 M NaCl, reaction with methyl viologen
1800
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hydrogen production, ferredoxin as electron donor
2998
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hydrogen oxidation, methylene blue as electron acceptor, hydrogenase II
4000
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hydrogen evolution, ferredoxin and 1 mM methyl viologen as electron donors
17600
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hydrogen oxidation, methylene blue as electron acceptor, hydrogenase II
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.8
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hydrogen evolution, hydrogenase II
6.3
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hydrogen evolution, hydrogenase I
6.9
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hydrogen evolution
7
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hydrogenase II, hydrogen oxidation, methylene blue as electron acceptor
8.4
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sulfur reductase activity
9.1
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hydrogen evolution, hydrogenase II
9.7
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hydrogen oxidation with methyl and benzyl viologen
9.8
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hydrogenase I, hydrogen oxidation
10.5
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hydrogenase II, hydrogen oxidation, methylene blue as electron acceptor
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 8
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pH 6.0: about 60% of maximal activity, pH 8.0: about 70% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
80
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sulfur reductase activity
90
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above 90C, hydrogenase II
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25 - 50
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25C: about 65% of maximal activity, 50: about 80% of maximal activity
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5
calculated from sequence
5.6
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isoelectric focusing
6
calculated from sequence
6.6
calculated from sequence
9.6
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isoelectric focusing
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
44500
-
gel filtration and SDS-PAGE
44600
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calculated from amino acid sequence
45000
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gel filtration
45100
-
calculated from amino acid sequence
45300
Chlorococcum submarinum
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calculated from amino acid sequence
45400
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calculated from amino acid sequence
47300
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isozyme HydA2, calculated from amino acid sequence
49000
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gel filtration
50000
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gel filtration
52000
-
SDS-PAGE
53000
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hydrogenase II, SDS-PAGE
53600
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calculated from amino acid sequence
57000
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gel filtration
60000
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gel filtration, hydrogenase I
60500
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SDS-PAGE
63800
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calculated from amino acid sequence
64300
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calculated from amino acid sequence
85000
Q8U0Z8 and Q8U0Z7 and Q8U0Z6
gel filtration, engineered minimal catalytically active 4-subunit subcomplex of respiratory membrane-bound hydrogenase
89000
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SDS-PAGE
98000
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gel filtration
100000
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native PAGE
110000
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native Ehb complex, gel filtration
122000
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native PAGE
130000
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gel filtration
185000
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gel filtration
320000
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gel filtration
360000
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Ehb complex, calculated from amino acid sequence
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
heterodimer
hexamer
monomer
octamer
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alpha, beta, gamma, delta, 2 * 52000 + 2 * 39000 + 2 * 30000 + 2 * 24000, SDS-PAGE
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2.15 A resolution, reduced, active form
-
crystals of the soluble form obtained using 20% polyethylene glycol 1500 as a precipitant, which belong to the monoclinic space group P21, with unit-cell parameters a = 60.57, b = 91.05, c = 66.85 A, beta = 101.46, to 2.4 A resolution. No crystals appear for the membrane form
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25
-
50% inactivation after 14 d
55
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50% inactivation after 1 h
90
Q8U0Z8 and Q8U0Z7 and Q8U0Z6
half-life of minimal catalytically active 4-subunit subcomplex of respiratory membrane-bound hydrogenase: 8 h. Half-life of the native 14-subunit membrane-bound respiratory membrane-bound hydrogenase complex
95
-
50% inactivation after 6 h, hydrogenase II
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
after treatment with 4 mM urea, 100% activity after several hours
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chelating agents protect against oxygen inactivation, 0.5 M EDTA allows 41% activity after 3 d in aqueous solution exposed to air
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in aqueous solutions at pH 8.0, under argon, nitrogen or hydrogen atmosphere, stable for many hours
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OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
air inactivation is reduced up to 25fold by adsoption on common anion exchange supports like DEAE cellulose, 3 mM Tris-HCl buffer pH 8
-
439680
rapid inactivation under aerobic conditions
the O2 sensitivities of minimal catalytically active 4-subunit subcomplex of respiratory membrane-bound hydrogenase and the native 14-subunit membrane-bound version are similar, half-lives of about 15 h in air
Q8U0Z8 and Q8U0Z7 and Q8U0Z6
730867
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-180C, 4 months, 100% activity
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-20C, several months, strictly anaerobical storage, little loss of activity
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-80C, several weeks, strictly anaerobical storage
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4C, under argon, 50% activity loss, 2 weeks
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5C, 5 d, strictly anaerobical storage
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crystals are stabilized with glycerol and stored under strict anaerobic conditions or in liquid nitrogen after flash-cooling
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
1284fold with a yield of 16.17%, by ultracentrifugation, ion exchange chromatography, gel filtration and hydrophobic-interaction chromatography
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aerobically purified hydrogenase is inactive and requires reductive activation
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aerobically using different ion-exchange chromatography columns
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affinity column chromatography with immobilised ferredoxin
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Ni-Sepharose 6 Fast Flow chromatography
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partially
partially, 40% pure
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Procion Red-agarose purification
purification of the engineered and expressed His-tagged 4-subunit cytoplasmic subcomplex of respiratory membrane-bound hydrogenase
Q8U0Z8 and Q8U0Z7 and Q8U0Z6
purified under aerobic conditions, requires reductive activation
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Q-sepharose HiLoad, hydroxyapatite, Superdex 200
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strictly under anaerobic conditions
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under anaerobic conditions, solubilized with n-dodecyl-beta-D-maltoside
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli
expressed in Escherichia coli BL21(DE3) cells
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
activation and de novo synthesis of the protein is inhibited by cycloheximide but not chloramphenicol
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D102K
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leads to lower binding free energies and higher association rate with [2Fe2S]-ferredoxin FDX1 and is thus a promising target for improving hydrogen production rates in engineered organisms
D102K/E221K
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double mutant enhances association rate constant
D102K/T99K
-
double mutant enhances association rate constant
E221K
-
higher association rate with [2Fe2S]-ferredoxin FDX1
M214K
-
least enhancement of association rate with [2Fe2S]-ferredoxin FDX1, destabilizes binding complexes
T99K
-
leads to lower binding free energies and higher association rate with [2Fe2S]-ferredoxin FDX1 and is thus a promising target for improving hydrogen production rates in engineered organisms
C42S
-
mutant enzyme with almost no activity in the reaction with H2 and oxidized benzyl viologen
C45S
-
mutants with about 5% of the wild-type activity in the reaction with H2 and oxidized benzyl viologen
C48S
-
mutant enzyme with almost no activity in the reaction with H2 and oxidized benzyl viologen
C73S
-
mutants with about 5% of the wild-type activity in the reaction with H2 and oxidized benzyl viologen
C76S
-
mutant enzyme with almost no activity in the reaction with H2 and oxidized benzyl viologen
C79S
-
mutants with about 5% of the wild-type activity in the reaction with H2 and oxidized benzyl viologen
C83S
-
mutant enzyme with approximately 10% of the activity of the wild-type enzyme in the reaction with H2 and oxidized benzyl viologen
additional information
Q8U0Z8 and Q8U0Z7 and Q8U0Z6
engineering and expressing of a His-tagged minimal catalytically active 4-subunit cytoplasmic subcomplex of respiratory membrane-bound hydrogenase. In order to obtain a minimal subcomplex, the native MBH operon is splitt it into two separate transcriptional units
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
biotechnology
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practical application in solar energy bioconversion
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