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Information on EC 1.12.99.6 - hydrogenase (acceptor)
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1.12.99.6 hydrogenase (acceptor)IUBMB Comments
Uses molecular hydrogen for the reduction of a variety of substances. Contains iron-sulfur clusters. The enzyme from some sources contains nickel.
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Word Map
- 1.12.99.6
- hydrogenases
-
h-cluster
- reinhardtii
- nitrogenase
- chlamydomonas
-
diiron
- ferredoxins
-
dithiolate
- desulfovibrio
- hydf
-
hupls
-
o2-tolerant
-
photoproduction
- eutropha
-
n2-fixing
-
diazotrophic
- acetobutylicum
-
electrocatalytic
-
subcluster
-
heterocystous
- pasteurianum
-
maturase
- nostoc
- f0f1-atpase
- fhl
-
h2-producing
-
syntrophic
-
h2-oxidizing
-
mixed-valence
-
photocatalytic
-
thiocapsa
-
hydrogen-producing
-
overpotential
-
biohydrogen
-
heterolytic
- h2ases
-
diphosphine
-
electrocatalysts
-
photobiological
-
hydrogen-oxidizing
-
oxygen-tolerant
- roseopersicina
-
nickel-containing
- cubane
-
organometallic
- desulfuricans
- brewing
- gallinae
- industry
The enzyme appears in viruses and cellular organisms
Synonyms
[fefe]-hydrogenase, uptake hydrogenase, hyda1, hydrogenase 3, hyd-1, hyd-2, fe-hydrogenase, hydrogenase 1, nife hydrogenase, hydrogenase 2, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
endo-hydrogenase
exo-hydrogenase
H2-sensing [NiFe] hydrogenase
HoxG
HupL
HupS
Hya
HycE
hydA
hydrogen-forming methylenetetrahydromethanopterin dehydrogenase
-
-
hydrogenase 2
hydrogenase 3
hydrogenase I (bidirectional)
-
catalyzes H2 oxidation and reduction at similar rates
hydrogenase II
Hyq
Mbh
membrane-bound [NiFe]-hydrogenase
Ni-Fe hydrogenase
NiFe hydrogenase
regulatory hydrogenase
respiratory hydrogenase
SHI
uptake hydrogenase
uptake [NiFe]-hydrogenase
[FeFe] hydrogenase
[FeFe]-H2ase
[FeFe]-hydrogenase
[FeFe]H2ase
[Fe]-hydA
Q2PWI0, Q2PWI3, Q2PWI4, Q2PWI5, Q2PWI6, Q2PWI7, Q2PWI9, Q2PWJ0, Q2PWJ8, Q38IH5, Q38IH6, Q38IH8, Q38IH9, Q38II3, Q38II4, Q38IJ1
-
[Fe]-hydrogenase
[Ni-Fe] hydrogenase
[NiFe] hydrogenase
[NiFe]-hydrogenase
hydA
Q2PWI0, Q2PWI3, Q2PWI4, Q2PWI5, Q2PWI6, Q2PWI7, Q2PWI9, Q2PWJ0, Q2PWJ8, Q38IH5, Q38IH6, Q38IH8, Q38IH9, Q38II3, Q38II4, Q38IJ1
-
hydrogenase 3
-
hydrogenase 3 is the large subunit of a [Ni-Fe]-type hydrogenase
hydrogenase 3
-
hydrogenase 3 is the large subunit of a [Ni-Fe]-type hydrogenase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
H2 + acceptor = reduced acceptor
-
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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PATHWAY SOURCE
PATHWAYS
BRENDA
MetaCyc
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SYSTEMATIC NAME
IUBMB Comments
hydrogen:acceptor oxidoreductase
Uses molecular hydrogen for the reduction of a variety of substances. Contains iron-sulfur clusters. The enzyme from some sources contains nickel.
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CAS REGISTRY NUMBER
COMMENTARY
9027-05-8
-
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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
H2 + 2,3,5-triphenyltetrazolium chloride
reduced 2,3,5-triphenyltetrazolium chloride
-
-
-
?
H2 + 2,3-dimethyl-1,4-naphthoquinone
2,3-dimethyl-naphthoquinol
-
-
-
?
H2 + anthraquinone 2,6-disulfonic acid
anthraquinol 2,6-disulfonic acid
-
-
-
?
H2 + oxidized 2,3-dimethylnaphthoquinone
2,3-dimethylnaphthoquinol
-
-
-
?
H2 + oxidized phenazine methosulfate
reduced phenazine methosulfate + H+
-
-
-
?
H2 + phenazine methosulfate
H+ + reduced phenazine methosulfate
-
best electron acceptor
-
?
H2 + acceptor
acceptor-H2
-
-
?
H2 + acceptor
acceptor-H2
-
Hyb is essential for hydrogen-dependent growth with a variety of electron acceptors, including Fe3+
-
?
H2 + acceptor
H+ + reduced acceptor
-
methylene blue acts as electron acceptor
-
?
H2 + acceptor
H+ + reduced acceptor
-
inactivation of hydrogenase genes impairs bacterial nitrogenase activity in Bradyrhizobium sp. (Vigna) and has an effect on total nitrogen content of the symbiotic plant partner, Vigna unguiculata. Hydrogenase activity might be necessary for optimal levels of nitrogenase activity in Bradyrhizobium sp. (Vigna) bacteroids
-
?
H2 + acceptor
H+ + reduced acceptor
-
2 different enzymes, hydrogenase I and II
-
r
H2 + acceptor
H+ + reduced acceptor
-
2 different enzymes, hydrogenase I and II
-
r
H2 + acceptor
H+ + reduced acceptor
-
methyl viologen acts as electron acceptor
-
r
H2 + acceptor
H+ + reduced acceptor
-
benzyl viologen acts as electron acceptor
-
?
H2 + acceptor
H+ + reduced acceptor
Cupriavidus necator H16 / ATCC 23440 / NCIB 10442 / S-10-1
-
-
-
?
H2 + acceptor
H+ + reduced acceptor
-
methyl viologen acts as electron acceptor
-
?
H2 + acceptor
H+ + reduced acceptor
-
methyl viologen acts as electron acceptor
-
r
H2 + acceptor
H+ + reduced acceptor
-
methylene blue acts as electron acceptor
-
?
H2 + acceptor
H+ + reduced acceptor
-
methyl viologen acts as electron acceptor
-
?
H2 + acceptor
H+ + reduced acceptor
-
methylene blue acts as electron acceptor
-
?
H2 + acceptor
H+ + reduced acceptor
-
enzyme is more active in hydrogen evolution than in hydrogen uptake
-
?
H2 + acceptor
H+ + reduced acceptor
-
reaction mechanism
-
?
H2 + acceptor
H+ + reduced acceptor
-
benzyl viologen, methylene blue and methylviologen can act as electron acceptors
-
?
H2 + acceptor
H+ + reduced acceptor
-
methylene blue acts as electron acceptor
-
r
H2 + acceptor
H+ + reduced acceptor
-
methylene blue, methyl viologen, methionaquinone, FMN and FAD can serve as electron acceptors, but not NAD+ or NADP+
-
?
H2 + acceptor
H+ + reduced acceptor
Hydrogenobacter thermophilus TK-6 / IAM 12695
-
methylene blue, methyl viologen, methionaquinone, FMN and FAD can serve as electron acceptors, but not NAD+ or NADP+
-
?
H2 + acceptor
H+ + reduced acceptor
-
2 different enzymes, hydrogenase I and II
-
r
H2 + acceptor
H+ + reduced acceptor
-
benzyl viologen, methylene blue, ferredoxin and methylviologen can act as electron acceptors
-
?
H2 + acceptor
H+ + reduced acceptor
-
ferredoxin acts as physiological electron donor
-
?
H2 + acceptor
H+ + reduced acceptor
Methanosarcina barkeri Fusaro / DSM 804
-
benzyl viologen, methylene blue, ferredoxin and methylviologen can act as electron acceptors
-
?
H2 + acceptor
H+ + reduced acceptor
Methanosarcina barkeri Fusaro / DSM 804
-
ferredoxin acts as physiological electron donor
-
?
H2 + acceptor
H+ + reduced acceptor
-
enzyme acts on artificial electron-accepting dyes, but is ineffective with pyridine nucleotides or other soluble physiological electron acceptors
-
?
H2 + acceptor
H+ + reduced acceptor
-
benzyl viologen, methyl viologen, NADPH and NADH can serve as electron donors
-
?
H2 + acceptor
H+ + reduced acceptor
-
methyl viologen acts as electron acceptor
-
r
H2 + acceptor
H+ + reduced acceptor
-
methylene blue acts as electron acceptor
-
r
H2 + acceptor
H+ + reduced acceptor
-
reduced ferredoxin can act as acceptor
-
r
H2 + acceptor
H+ + reduced acceptor
-
ferredoxin acts as physiological electron donor
-
?
H2 + acceptor
H+ + reduced acceptor
-
Hya can oxidize both exogenously added H2 and formate hydrogen lyase-evolved H2 anaerobically
-
?
H2 + acceptor
H+ + reduced acceptor
-
Hya can oxidize both exogenously added H2 and formate hydrogen lyase-evolved H2 anaerobically
-
?
H2 + acceptor
H+ + reduced acceptor
-
benzyl viologen acts as electron acceptor
-
?
H2 + acceptor
H+ + reduced acceptor
-
methyl viologen acts as electron acceptor
-
?
H2 + acceptor
H+ + reduced acceptor
-
methyl viologen and benzyl viologen can serve as electron acceptors
-
?
H2 + methenyltetrahydromethanopterin
H+ + methylenetetrahydromethanopterin
-
the heterolytic cleavage of H2 by the enzyme is dependent on the presence of methenyltetrahydromethanopterin
-
r
H2 + methenyltetrahydromethanopterin
H+ + methylenetetrahydromethanopterin
-
the presence of methenyltetrahydromethanopterin is essentially required for H2 activation by [Fe] hydrogenase
-
r
H2 + methyl viologen
H+ + reduced methyl viologen
-
-
-
?
H2 + oxidized acceptor
H+ + reduced acceptor
-
almost 100% of the membrane-attached MBH is reversibly redox-active
-
?
H2 + oxidized acceptor
H+ + reduced acceptor
-
[NiFeSe]-hydrogenase is a highly efficient H2 cycling catalyst
-
?
H2 + oxidized acceptor
H+ + reduced acceptor
-
heterolytic H2 cleavage, with one hydrogen ending up as a bridging hydride and one as a proton on a cysteine ligand, which has a barrier slightly too high to be compatible with measured catalytic turnover rates. Alternative mechanisms suggest heterolytic cleavage as an initial step to generate a complex with nickel in oxidation state Ni(I). In the following cycles, H2 is instead cleaved on nickel using an oxidative addition mechanism with a lower barrier
-
?
H2 + oxidized acceptor
H+ + reduced acceptor
Q2PWI0, Q2PWI3, Q2PWI4, Q2PWI5, Q2PWI6, Q2PWI7, Q2PWI9, Q2PWJ0, Q2PWJ8, Q38IH5, Q38IH6, Q38IH8, Q38IH9, Q38II3, Q38II4, Q38IJ1
-
-
?
H2 + oxidized benzyl viologen
H+ + reduced benzyl viologen
-
-
-
?
H2 + oxidized benzyl viologen
H+ + reduced benzyl viologen
-
-
-
?
H2 + oxidized benzyl viologen
H+ + reduced benzyl viologen
-
-
-
?
H2 + oxidized benzyl viologen
H+ + reduceded benzyl viologen
-
-
-
r
H2 + oxidized benzyl viologen
H+ + reduceded benzyl viologen
-
-
-
r
H2 + oxidized benzyl viologen
H+ + reduceded benzyl viologen
-
-
-
r
H2 + oxidized benzyl viologen
H+ + reduceded benzyl viologen
-
-
-
r
H2 + oxidized benzyl viologen
reduced benzyl viologen + H+
-
-
-
?
H2 + oxidized benzyl viologen
reduced benzyl viologen + H+
-
-
-
r
H2 + oxidized benzyl viologen
reduced benzyl viologen + H+
-
there is at least one autocatalytic reaction step in the hydrogenase-catalyzed reaction
-
?
H2 + oxidized dichloroindophenol
H+ + reduced dichloroindophenol
-
-
-
?
H2 + oxidized dichloroindophenol
H+ + reduced dichloroindophenol
-
-
-
?
H2 + oxidized electron acceptor
H+ + reduced electron acceptor
-
-
-
?
H2 + oxidized electron acceptor
H+ + reduced electron acceptor
-
both platinum and pyrolytic graphite edge/HydA electrodes are effective catalysts operating near the reversible potential of the H+/H2 redox couple
-
?
H2 + oxidized electron acceptor
H+ + reduced electron acceptor
-
-
-
?
H2 + oxidized electron acceptor
H+ + reduced electron acceptor
-
-
-
?
H2 + oxidized electron acceptor
H+ + reduced electron acceptor
-
-
-
?
H2 + oxidized methionaquinone
reduced methionaquinone
Hydrogenobacter thermophilus TK-6 / IAM 12695
-
-
-
r
H2 + oxidized methyl viologen
H+ + reduced methyl viologen
Aeropyrum camini SY1 / ATCC BAA-758 / DSM 16960 / JCM 2091
-
-
-
?
H2 + oxidized methyl viologen
H+ + reduced methyl viologen
-
-
-
?
H2 + oxidized methyl viologen
H+ + reduced methyl viologen
-
-
-
?
H2 + oxidized methyl viologen
H+ + reduced methyl viologen
-
-
-
?
H2 + oxidized methyl viologen
H+ + reduced methyl viologen
-
-
-
?
H2 + oxidized methyl viologen
H+ + reduced methyl viologen
-
-
-
?
H2 + oxidized methyl viologen
H+ + reduced methyl viologen
-
-
-
?
H2 + oxidized methyl viologen
H+ + reduced methyl viologen
Tetraselmis sp. KSN-2002 NCIM 1605
-
-
-
?
H2 + oxidized methyl viologen
H+ + reduced methyl viologen
-
-
-
?
H2 + oxidized methyl viologen
reduced methyl viologen + H+
-
-
-
?
H2 + oxidized methyl viologen
reduced methyl viologen + H+
-
-
-
?
H2 + oxidized methyl viologen
reduced methyl viologen + H+
-
-
-
?
H2 + oxidized methyl viologen
reduced methyl viologen + H+
-
-
-
r
H2 + oxidized methyl viologen
reduced methyl viologen + H+
-
-
-
r
H2 + oxidized methylene blue
H+ + reduced methylene blue
-
-
-
?
H2 + oxidized methylene blue
H+ + reduced methylene blue
-
-
-
?
H2 + oxidized methylene blue
reduced methylene blue + H+
-
-
-
?
H2 + oxidized sodium hydrosulfite
H+ + reduced sodium hydrosulfite
-
-
-
?
H2 + oxidized sodium hydrosulfite
H+ + reduced sodium hydrosulfite
-
-
-
?
additional information
?
-
-
although the HoxF subunit contains binding sites for flavin mononucleotide and NAD(H), cell-free extracts of Allochromatium vinosum does not catalyse a H2-dependent reduction of NAD+
-
?
additional information
?
-
-
the catalytic bias, i.e. the ratio of maximal rates in the two directions is not mainly determined by redox properties of the active site, but rather by steps which occur on sites of the proteins that are remote from the active site
-
?
additional information
?
-
-
the enzyme exhibits both proton-reducing and H2-oxidizing activities
-
?
additional information
?
-
-
no activity is observed using NAD+, 2,3-dimethoxy methyl-1,4-benzoquinone, and potassium ferricyanide as electron acceptors
-
?
additional information
?
-
-
no activity is observed using NAD+, 2,3-dimethoxy methyl-1,4-benzoquinone, and potassium ferricyanide as electron acceptors
-
?
additional information
?
-
-
a diiron dithiolate complex holding a micro-hydride on the iron atoms and a proton on the basic site of a chelating diphosphine ligand as a structural model of the [FeFe]-hydrogenase active site. The pendant base in the phosphine ligand may play a similar role to the proton-transfer relay as the bridging N in a diiron azadithiolate complex does
-
?
additional information
?
-
-
oxidation of hexacarbonyl(1,3-dithiolato-S,S')diiron complexes with varying amounts of dimethyldioxirane as mimics of the active site of [FeFe]-hydrogenase. Chemoselectivity of the oxidation products depends upon the substituent R (R=H, Me, 1/2 (CH2)5)
-
?
additional information
?
-
-
protonation of a model of the subsite of [FeFe]-hydrogenase, [Fe2(micro-pdt)(CO)4(PMe3)2]. The deceptively simple stoichiometric reaction is limited by the rate of protonation of the basal-apical isomer followed by its rearrangement to the transoid basal form
-
?
additional information
?
-
-
study on the catalytic mechanism of an active-site model of [Fe] hydrogenase by small modifications of the first ligand shell. Dispersion interactions between the active site and the hydride acceptor methenyltetrahydromethanopterin render the hydride transfer step less endergonic and lower its barrier. Substitution of CO by CN-, which resembles [FeFe] hydrogenase-like coordination, inverts the elementary steps H- transfer and H2 cleavage. The catalytic efficiency of [Fe] hydrogenase can be attributed to a flat energy profile throughout the catalytic cycle. Intermediates that are too stable, as they occur, e.g., when one CO ligand is substituted by CN-, significantly slow down the turnover rate of the enzyme. The catalytic activity of the wild-type form of the active-site model could, however, be enhanced by a PH3 ligand substitution of the CO ligand
-
?
additional information
?
-
-
hydrogenase during its reaction cycle has an autocatalytic step
-
?
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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 + acceptor
acceptor-H2
-
-
-
?
H2 + acceptor
H+ + reduced acceptor
-
inactivation of hydrogenase genes impairs bacterial nitrogenase activity in Bradyrhizobium sp. (Vigna) and has an effect on total nitrogen content of the symbiotic plant partner, Vigna unguiculata. Hydrogenase activity might be necessary for optimal levels of nitrogenase activity in Bradyrhizobium sp. (Vigna) bacteroids
-
-
?
H2 + acceptor
H+ + reduced acceptor
-
2 different enzymes, hydrogenase I and II
-
r
H2 + acceptor
H+ + reduced acceptor
-
reaction mechanism
-
-
?
H2 + acceptor
H+ + reduced acceptor
-
ferredoxin acts as physiological electron donor
-
-
?
H2 + acceptor
H+ + reduced acceptor
Methanosarcina barkeri Fusaro / DSM 804
-
ferredoxin acts as physiological electron donor
-
-
?
H2 + acceptor
H+ + reduced acceptor
-
ferredoxin acts as physiological electron donor
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
iron-sulfur centre
-
contains a mononuclear iron coordinated by the sulfur of cysteine 176, the iron center is the catalytically active constituent of an iron guanylyl pyridone cofactor
iron-sulfur centre
-
contains one [2Fe-2S] and three [4Fe-4S] clusters
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CN-
CO
Fe
Fe2+
Iron
Ni
Ni2+
Sulfide
additional information
-
no increase in the hydrogenase activity is observed in response to ferric sulfate, ferric citrate, ferric ammonium citrate, and ferric nitrate
CN-
-
the auxiliary proteins HoxL and HoxV assist in assembly of the Fe(CN-)2CO moiety
CN-
-
the catalytic center is equipped with 1.8 CN- per protein molecule
CO
-
the auxiliary proteins HoxL and HoxV assist in assembly of the Fe(CN-)2CO moiety
Fe
-
Ni-Fe active site. Presence of eight Fe-S clusters, three [2Fe-2S] clusters and five [4Fe-4S] clusters
Fe
-
lacks the ferredoxin-like clusters, but contains the H-cluster [Fe4S4] component
Fe
-
the HydA1 H-cluster consists of a [4Fe4S] cluster and a diiron site, 2FeH
Fe
-
iron-sulfur cluster as well as 4Fe-4S-ferredoxin-type cluster
Fe
-
the large subunit HoxC is purified without its small subunit. Two forms of HoxC are identified. Both forms contain iron but only substoichiometric amounts of nickel. One form is a homodimer of HoxC whereas the second also contains the Ni–Fe site maturation proteins HypC and HypB. Despite the presence of the Ni–Fe active site in some of the proteins, both forms, which lack the Fe–S clusters normally present in hydrogenases, cannot activate hydrogen. The incomplete insertion of nickel into the Ni–Fe site provides direct evidence that Fe precedes Ni in the course of metal center assembly
Fe
-
is composed of a small subunit, capable in coordinating one [3Fe4S] and two [4Fe4S] clusters
Fe
-
the auxiliary proteins HoxL and HoxV assist in assembly of the Fe(CN-)2CO moiety
Fe
-
[FeFe]-hydrogenase.The H cluster (hydrogen-activating cluster) contains a di-iron centre ([2Fe]H subcluster, a (L)(CO)(CN)Fe(mu-RS2)(mu-CO)Fe (CysS)(CO)(CN) group) covalently attached to a cubane iron-sulphur cluster ([4Fe-4S]H subcluster). The added redox equivalent not only affects the [4Fe-4S]H subcluster, but also the di-iron centre
Fe
-
specific protein-protein interactions of maturation proteins may be required during [FeFe] cluster synthesis and/or insertion. Maturation proteins HydE and HydG interact with the [FeFe] hydrogenase large subunit HydA, which binds the H-cluster. Neither HydE nor HydG interact with the [FeFe] hydrogenase small subunit, HydB. No interaction of HydF, which catalyzes an energy-dependent step during H-cluster assembly or insertion, with either HydA or HydB
Fe
-
the Hred form is assigned as a mixture of an Fe(I)Fe(I) form with an open site on the distal iron center and either a Fe(I)Fe(I) form in which the distal cyanide is protonated or a Fe(II)Fe(II) form with a bridging hydride ligand. The Hox form is assigned as a valence-localized Fe(I)Fe(II) redox level with an open site at the distal iron. The Hox air form is assigned as an Fe(II)Fe(II) redox level with OH- or OOH- bound to the distal iron center that may or may not have an oxygen atom bound to one of the sulfur atoms of the dithiolate linker
Fe
-
the Hred form is assigned as a mixture of an Fe(I)Fe(I) form with an open site on the distal iron center and either a Fe(I)Fe(I) form in which the distal cyanide is protonated or a Fe(II)Fe(II) form with a bridging hydride ligand. The Hox form is assigned as a valence-localized Fe(I)Fe(II) redox level with an open site at the distal iron. The Hox air form is assigned as an Fe(II)Fe(II) redox level with OH- or OOH- bound to the distal iron center that may or may not have an oxygen atom bound to one of the sulfur atoms of the dithiolate linker
Fe
-
membrane-bound [NiFe]-hydrogenase exhibits prominent electron paramagnetic resonance signals originating from [3Fe–4S]1 and [4Fe–4S]1 clusters
Fe
-
iron center octahedrally coordinated by one dithiothreitol-sulfur and one dithiothreitol-oxygen, two CO, the nitrogen of 2-pyridinol and the 6-formylmethyl group of 2-pyridinol in an acyliron ligation
Fe
-
iron azadithiolate phosphine-substituted complex and its protonated species featuring the NH proton and/or bridging Fe hydride, [Fe2(micro-S(CH2)2NnPr(H)m(CH2)2S)(micro-H)n(CO)4(PMe3)2]2 (2m+2n)+, mimic the active site of Fe-only hydrogenase. The ability to accept protons for the aza nitrogen and the Fe sites is essential for the enzymatic H2 production at the mild potential
Fe
-
protonation can take place in a terminal fashion at a single Fe or by bridging between two iron centres, protonation of a model of the subsite of [FeFe]-hydrogenase, [Fe2(m-pdt)(CO)4(PMe3)2], occurs via a two-step mechanism
Fe
-
protonation of diiron dithiolato complexes can occur at a single Fe site, even for symmetrical (FeI)2 compounds. The terminal hydride [HFe2(S2C3H6)(CO)2(dppv)2]+ catalyzes proton reduction at potentials 200 mV milder than the isomeric bridging hydride, thereby establishing a thermodynamic advantage for catalysis operating via terminal hydride
Fe
-
the Fe(CO)2(Pi-Pr3) site is rotated in solution, driven by steric factors. Fe atom featuring a vacant apical coordination position is an electrophilic Fe(I) center. One-electron oxidation of [Fe2(S2C2H4)(CN)(CO)3(dppv)]- results in 2e oxidation of 0.5 equiv to give the micro-cyano derivative [FeI2(S2C2H4)(CO)3(dppv)](micro-CN)[FeII2(S2C2H4)(micro-CO)(CO)2(CN)(dppv)]
Fe
-
has Fe-S clusters, contains 10 g atoms of Fe per mol of protein
Fe
-
the electron acceptor interacts only with the [FeS]distal cluster in the hydrogenase, and accordingly the autocatalyst is a hydrogenase form in which the [FeS]distal cluster holds an electron (i.e., at least the [FeS]distal cluster is reduced)
Fe2+
-
essential element for the assembly and maturation, the addition of Fe-EDTA (0.05 mM) does not affect the level of hydrogenase activity
Fe2+
-
1 mM increases hydrogenase activity 4fold, is not sufficient to increase hydrogenase activities without S-adenosyl methionine and the standard 20 L-amino acids
Fe2+
-
the active site has a characteristic bis(micro-thiolato)NiFe unit, where the Ni atom and the Fe atom are bridged by an undetermined oxygen-bearing ligand. This ligand probably derives from the aqueous solvent and is therefore most likely to be H2O, OH- or O2-. A NiFe complex is not able to activate H2 when coordinated with an CH3CN ligand, thus a highly labile ligand that is simultaneously able to act as a Lewis base for the heterolytic activation of H2 is crucial to the action of H2ase. The CH3CN-coordinated Ni(II)Fe(II) complex is unstable in the presence of water and decomposed to the Ni(II) complex and the Fe(II) complex via the Fe-S bond cleavage in water. In order to synthesise H2O-coordinated NiFe complexes in aqueous media, the Lewis acidity of the Fe centre must be increased to form strong Fe-S bonds. Thus, organometallic ligands with a back-donating character to form Fe-C bonds are required
Iron
-
within the catalytic centre one carbonyl and two cyanide ligands are covalently attached to the iron
Iron
-
the enzyme harbors an iron-containing cofactor, in which a lowspin iron is complexed by a pyridone, two CO and a cysteine sulfur, [Fe] hydrogenase apoenzyme is converted completely into [Fe] hydrogenase holoenzyme by mixing the apoenzyme with a 3fold excess of the iron-containing [Fe] hydrogenase cofactor
Iron
contains 0.23 Fe atoms per molecule of large subunit HyhL
Ni
-
[NiFe] hydrogenase has two different oxidized states, Ni-A (unready, exhibits a lag phase in reductive activation) and Ni-B (ready). Ni-B possesses a monatomic nonprotein bridging ligand at the Ni-Fe active site, whereas Ni-A has a diatomic species
Ni
-
Rhizobium leguminosarum biovar viciae symbiotic hydrogenase activity and processing are limited by the level of nickel in agricultural soils
Ni2+
-
essential element for the assembly and maturation, addition of 0.1 mM Ni2+ to the growth medium significantly enhances the hydrogenase activity. Nickel-treatment affects the level of the protein, but not the mRNA
Ni2+
-
is composed of a large subunit, harboring the [NiFe] active site
Ni2+
-
Ni-Fe active site assembly, nickel is absent in samples of HoxV
Ni2+
-
the active site has a characteristic bis(micro-thiolato)NiFe unit, where the Ni atom and the Fe atom are bridged by an undetermined oxygen-bearing ligand. This ligand probably derives from the aqueous solvent and is therefore most likely to be H2O, OH- or O2-. A NiFe or NiRu complex are not able to activate H2 when coordinated with an CH3CN ligand, thus a highly labile ligand that is simultaneously able to act as a Lewis base for the heterolytic activation of H2 is crucial to the action of H2ase. The CH3CN-coordinated Ni(II)Fe(II) complex is unstable in the presence of water and decomposed to the Ni(II) complex and the Fe(II) complex via the Fe-S bond cleavage in water. In order to synthesise H2O-coordinated NiFe complexes in aqueous media, the Lewis acidity of the Fe centre must be increased to form strong Fe-S bonds. Thus, organometallic ligands with a back-donating character to form Fe-C bonds are required
Ni2+
-
accessory protein HypB is necessary for Ni(II) incorporation into the hydrogenase protein. HypB has two metal-binding sites, a high-affinity Ni(II) site that includes ligands from the N-terminal domain and a low-affinity metal site located within the C-terminal GTPase domain
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1-ethyl-3-(3-dimethylaminopropyl) carbodiimide
-
8 residues modified by 0.5 mM in the presence of 30 mM nitrotyrosine ethylester
5-5'dithiobis-(2-nitrobenzoate)
-
chemical modification of cysteine residues, 8 residues modified by 0.5 mM. 16 residues modified in the presence of 2% sodium dodecyl sulfate. 20 residues modified by 1 mM and in the presence of urea, EDTA, NaBH4
N-bromosuccinimide
-
complete inactivation at 10 mM, 20% inactivation at 0.1 mM
CO
-
bond length alterations after incubation of HydA1 with CO and H2, related to structural and oxidation state changes at the catalytic Fe atoms, e.g., to the binding of an exogenous CO at 2FeH in CO-inhibited enzyme
CO
-
binds irreversibly, hydrogenase I has a lower affinity for CO than hydrogenase II
CO
-
noncompetitive vs. oxidized methyl viologen, competitive vs. H2
CO
-
the bis(PMe3) nitrosyl complexes readily undergo CO substitution to give the (PMe3)3 derivatives
Cu2+
-
65% loss of activity after 2 min at 0.005 mM, complete inhibition at 0.1 mM in the presence of ascorbate, no inhibition observed without ascorbate
O2
-
maintains 100% of its initial activity after a 48 h exposure to air, after 120 and 168 h exposures, the residual activities are 90% and 75%, respectively. It is very tolerant to oxygen
O2
-
non competitive versus methylene blue, uncompetitive versus H2, reversibility is time-dependent, inhibition is protected by H2
O2
-
the direct interaction of the [2Fe]H subsite with dioxygen is an exothermic and specific reaction in which O2 most favorably binds in an end-on manner to the distal iron. Irreversibility of dioxygen-induced enzyme inactivation by water release and degradation of the ligand environment of the H-cluster
O2
-
reacts with the enzyme, reversibly, causing inactivation. Although traces of O2 (less than 1%) rapidly and completely remove H2 oxidation activity, the enzyme sustains partial activity for H2 production even in the presence of 1% O2 in the atmosphere. O2 tolerance of the [NiFeSe]-hydrogenase is greater at higher temperature
O2
-
enzyme is quite stable under air atmosphere, half-life of activity is ca. 48 h at 4°C, inactivation is irreversible
O2
-
the enzyme is irreversibly inhibited under aerobic conditions
O2
-
exhibits 80% residual activity after exposure to air for 24 h, decreases to 75% and 37% after 48 and 72 h exposures, respectively. After a 96 h exposure, activity is undetectable. The enzyme is oxygen sensitive
additional information
-
loss of Fe-Fe distances in protein purified under mildly oxidizing conditions, partial degradation of the H-cluster
-
additional information
-
immobilization of synthetic analogues of the [FeFe]H2ase active site on polyethyleneglycol-rich polystyrene beads
-
additional information
-
isomerization of the terminal hydride is inhibited both by the basicity of the Fe2 complex as well as by the steric size of the dithiolate in the models. In the enzyme, terminal-bridge isomerization may also be inhibited by hydrogen bonding between CNdistal and a epsilon-ammonium center of a nearby, highly conserved lysine residue
-
additional information
-
front velocity decreases on increase of the electron acceptor benzyl viologen concentration at all measured hydrogenase concentrations
-
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
3,4-dihydroxy-L-phenylalanine
-
substitutes for tyrosine to stimulate in vitro HydA1 activation, improves HydA1 maturation 4fold
HoxL
-
the auxiliary protein HoxL participates specifically in the maturation of the large subunit of the enzyme. It is essential for H2-oxidizing activity and enzyme-driven growth on H2. HoxL acts as a specific chaperone assisting the transfer of the Fe(CN-)2CO cofactor intermediate from the Hyp machinery to the enzyme
-
HoxV
-
the auxiliary protein HoxL participates specifically in the maturation of the large subunit of the enzyme. It is essential for H2-oxidizing activity and enzyme-driven growth on H2. HoxV functions as a scaffold delivering the Fe(CN-)2CO moiety to the precursor of the large subunit pre-HoxG of the enzyme
-
HydEF
-
maturase, role in biosynthesis of the active site. HydEF and hydG, coexpressed with the structural genes hydA1 and hydA2 in Escherichia coli lead to active [FeFe]-hydrogenase
-
HypB
-
accessory protein HypB is necessary for the production of active hydrogenase
-
S-adenosyl methionine
-
exogenous S-adenosyl methionine stimulates in vitro hydrogenase activation, but does not individually enhance hydrogenase activation. 2 mM increases hydrogenase activity 4fold
Sulfide
-
1 mM increases hydrogenase activity 4fold, is not sufficient to increase hydrogenase activities without S-adenosyl methionine and the standard 20 L-amino acids
HydE
-
from Clostridium acetobutylicum extracts, activation of HydADELTAEFG requires the presence of a preformed [4Fe-4S] cluster on HydA
-
HydE
-
is required to synthesize and assemble the active site utilizing Escherichia coli metabolites
-
HydF
-
from Clostridium acetobutylicum extracts, activation of HydADELTAEFG requires the presence of a preformed [4Fe-4S] cluster on HydA
-
HydF
-
is required to synthesize and assemble the active site utilizing Escherichia coli metabolites
-
HydG
-
from Clostridium acetobutylicum extracts, activation of HydADELTAEFG requires the presence of a preformed [4Fe-4S] cluster on HydA
-
HydG
-
maturase, role in biosynthesis of the active site. HydEF and hydG, coexpressed with the structural genes hydA1 and hydA2 in Escherichia coli lead to active [FeFe]-hydrogenase
-
HydG
-
is required to synthesize and assemble the active site utilizing Escherichia coli metabolites
-
additional information
-
guanosine triphosphate does not improve hydrogenase maturation
-
additional information
-
tyrosine enhances in vitro maturation of HydA1 hydrogenase. Tyrosine has the most significant effect on overall HydA1 activities. Cysteine enhances in vitro maturation of HydA1 hydrogenase. Cysteine has the most significant effect on early HydA1 activities
-
additional information
-
activity increases up to 2.5fold during incubation at 50°C under H2
-
additional information
-
nitrosyl complexes reduce at potentials that are ca. 1 V milder than their carbonyl counterparts, NO+ forms diiron dithiolates that are not isostructural with the corresponding carbonyl complexes and that display enhanced Lewis acidity
-
additional information
-
front velocity increases as the overall enzyme concentration (and hence the concentration of the autocatalyst form of the enzyme) is increased
-
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
Km for various electron donors
-
0.000047
H2
-
apparent value, pH and temperature not specified in the publication
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1500 - 9000
Abz-VAA
-
NiFe hydrogenase attached to a pyrolytic graphite electrode
additional information
additional information
-
turnover number for various electron donors
-
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.008
-
hydrogen uptake specific activity of the hydrogenase 3 lacking mutant enzyme HD705/pBS(Kan), using methyl viologen as a substrate
0.035
-
hydrogen uptake specific activity of the wild type enzyme, using methyl viologen as a substrate
1078
-
after 152fold purification, at 55°C, pH 7.0, using phenazine methosulfate as electron acceptor
2
-
crude extract, at 55°C, pH 7.0, using methylene blue as electron acceptor
30
-
after 152fold purification, at 55°C, pH 7.0, using dichloroindophenol as electron acceptor
300
344
-
after 152fold purification, at 55°C, pH 7.0, using methylene blue as electron acceptor
484
-
after 152fold purification, at 80°C, pH 7.0, using methylene blue as electron acceptor
50
55
-
after 152fold purification, at 55°C, pH 7.0, using methyl viologen as electron acceptor
80
additional information
additional information
-
specific activities with various electron donors
additional information
-
evaluation of hydrogenase activities in Enterobacter aerogenes with respect to H2 evolution and its uptake by using intact cells and appropriate surfactants
additional information
-
specific activities with various electron donors
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5.5 - 6.5
-
the steady-state current caused by catalytic uptake of hydrogen is maximal at pH 5.5-6.5 under overvoltage of 30-60 mV
5.9
-
the maximum H2 oxidation current increases as the pH is raised from 4.3 to 5.9
6 - 6.5
-
the steady-state current caused by catalytic uptake of hydrogen is maximal at pH 6.0-6.5 under overvoltage of 30-60 mV
7.5
8.5
additional information
-
solubilization of the imer is associated with a downshift of the optimum pH for H2-oxidizing activity
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
4.3 - 8.4
-
the maximum H2 oxidation current increases as the pH is raised from 4.3 to 5.9, then it is constant up to pH 8.4
5.5 - 9
-
H2 oxidation, pH 5.5: 40% of maximal activity, pH 9: 60% of maximal activity
6 - 11
-
almost no activity at pH 6.0, approx. 30% of maximal activity at pH 11.0
6 - 9
-
optimal pH range for the hydrogen oxidation activity is 8.5 to 9.0, optimal pH range for the proton reduction activity is 6.0 to 6.5
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
60
80
-
at pH 6.0, using 10 mM methyl viologen or 20 mM sodium hydrosulfite as electron acceptors
85
85
-
optimal temperature for the hydrogen oxidation activity and for the proton reduction activity
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
10 - 90
-
at 90°C the enzyme retains 83% of maximum activity, at lower temperatures hydrogenase activity remains the same as at 10°C (13% of maximum activity), similar activity is observed between 40 and 60°C (about 70% of maximum activity)
20 - 95
-
almost no activity at 20°C, approx. 20% of maximal activity at 95°C
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
calculated isoelectric point of the HoxU subunit is 7.5
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Cronbergia siamensis SAG 11.82 TISTR 8012