MetaCyc Enzyme: bifurcating [FeFe]-hydrogenase (soluble)

Synonyms: trimeric [FeFe] hydrogenase, Fe-hydrogenase

Superclasses: a hydrogenasean [FeFe] hydrogenase

Species: Thermotoga maritima

Subunit composition of bifurcating [FeFe]-hydrogenase (soluble) = [HydA][HydB][HydC]
         hydrogenase α subunit = HydA (summary available)
         hydrogenase β subunit = HydB (summary available)
         hydrogenase γ subunit = HydC (summary available)

General Background

Hydrogenases catalyze the reversible interconversion of protons, electrons and H2, resulting in H2 oxidation to two protons or in the reverse direction, molecular hydrogen production by the reduction of protons.

Most hydrogenases are metalloenzymes that contain iron-sulfur clusters. They have been subdivided into two main classes based on the composition of two metal atoms at their active center: [NiFe] hydrogenases and [FeFe] hydrogenases. These two classes are phylogenetically distinct. It should be noted that in some of the [NiFe] hydrogenases one of the Ni-bound cysteine residues is replaced by selenocysteine. Those enzymes are known as [NiFeSe] hydrogenases. The [FeFe] hydrogenases usually have high catalytic activity, but are sensitive to irreversible inactivation by oxygen, more so than [NiFe] hydrogenases.

While [FeFe] hydrogenases are limited to certain bacteria and a few unicellular eukaryotes, [NiFe] hydrogenases are widespread in both bacteria and archaea [Sun10].

[NiFe] hydrogenases are usually heterodimeric proteins, but can be associated with additional subunits.The large subunit contains the [NiFe] catalytic site, while the smaller subunit contains 3 FeS clusters. These clusters transfer electrons from an external electron donor to the [NiFe] site for reduction of protons [Sun10]. Many [FeFe]-hydrogenases are monomeric but possess additional domains that contain FeS clusters [Vignais08]. The catalytic core of [FeFe] hydrogenases is a single domain of about 350 residues that accommodates the active site known as the H cluster.

In addition, a third class of hydrogenases is found in some methanogenic archaea. These enzymes contain only a mononuclear Fe active site and no FeS clusters, and are known as [Fe] hydrogenases.

About This Enzyme

The hydrogenase from Thermotoga maritima is an iron-only [FeFe] enzyme. It is comprised of three subunits: the hydrogenase α subunit contains the catalytic H-cluster, three 4Fe-4S clusters and two 2Fe-2S clusters; the hydrogenase β subunit contains three 4Fe-4S clusters and one 2Fe-2S cluster, and the hydrogenase γ subunit contains one 2Fe-2S cluster [Schut09]. Tungsten can increase the cellular concentration of the enzyme and its in vitro cellular activity 10 fold [Juszczak91].

Electron bifurcation is proposed to be a type of energy conservation, in addition to substrate level phosphorylation and respiration [Herrmann08]. The [FeFe] hydrogenase from Thermotoga maritima is proposed to be a bifurcating enzyme because it promotes exergonic oxidation of reduced ferredoxin to drive the unfavorable oxidation of NADH to produce H2, using electron bifurcation. The proposed bifurcating [FeFe] hydrogenase of Thermotoga maritima therefore requires both NADH and reduced ferredoxin as simultaneous electron donors [Schut09]. The hydrogenase β subunit contains the NADH and an FMN binding site and is potentially the site of NADH oxidation. The hydrogenase γ subunit is proposed to be the site of ferredoxin oxidation.

Gene-Reaction Schematic

Gene-Reaction Schematic

Revised 07-May-2010 by Caspi R, SRI International
Revised 07-Mar-2011 by Weerasinghe D

Enzymatic reaction of: hydrogenase

Inferred from experiment

Synonyms: Fe-hydrogenase, iron-hydrogenase

EC Number:

2 an oxidized ferredoxin [iron-sulfur] cluster + NAD+ + 2 H2 ← 2 a reduced ferredoxin [iron-sulfur] cluster + NADH + 3 H+

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the Enzyme Commission system.

The reaction is irreversible in the opposite direction.

In Pathways: hydrogen production I

Cofactors or Prosthetic Groups: a [2Fe-2S] iron-sulfur cluster [Verhagen99], a [4Fe-4S] iron-sulfur cluster [Verhagen99]

Activators (Unknown Mechanism): W+6 [Juszczak91]

Subunit of bifurcating [FeFe]-hydrogenase (soluble): hydrogenase α subunit

Synonyms: HydA

Gene: hydA Accession Numbers: G-235 (MetaCyc), TM_1426

Locations: cytosol

Molecular Weight: 72.248 kD (from nucleotide sequence)

GO Terms:
Cellular Component:
GO:0005829 - cytosol []

Unification Links: Protein Model Portal:O52683, UniProt:O52683

Relationship Links: InterPro:IN-FAMILY:IPR000283, InterPro:IN-FAMILY:IPR001041, InterPro:IN-FAMILY:IPR001450, InterPro:IN-FAMILY:IPR003149, InterPro:IN-FAMILY:IPR004108, InterPro:IN-FAMILY:IPR009016, InterPro:IN-FAMILY:IPR012336, InterPro:IN-FAMILY:IPR017896, InterPro:IN-FAMILY:IPR017900, InterPro:IN-FAMILY:IPR019574, Pfam:IN-FAMILY:PF00037, Pfam:IN-FAMILY:PF00111, Pfam:IN-FAMILY:PF02256, Pfam:IN-FAMILY:PF02906, Pfam:IN-FAMILY:PF10588, Pfam:IN-FAMILY:PF12837, Prosite:IN-FAMILY:PS00198, Prosite:IN-FAMILY:PS00641, Prosite:IN-FAMILY:PS51085, Prosite:IN-FAMILY:PS51379, Smart:IN-FAMILY:SM00902, Smart:IN-FAMILY:SM00929

This subunit contains the catalytic H-cluster, three 4Fe-4S clusters and two 2Fe-2S clusters. Potentially the site of the trimeric enzyme's hydrogenase activity.

Citations: [Verhagen99, Schut09]

Subunit of bifurcating [FeFe]-hydrogenase (soluble): hydrogenase β subunit

Synonyms: HydB

Gene: hydB Accession Numbers: G-236 (MetaCyc), TM_1425

Locations: cytosol

Molecular Weight: 68.676 kD (from nucleotide sequence)

GO Terms:
Cellular Component:
GO:0005829 - cytosol []

Unification Links: Protein Model Portal:O52682, UniProt:O52682

Relationship Links: InterPro:IN-FAMILY:IPR001450, InterPro:IN-FAMILY:IPR001949, InterPro:IN-FAMILY:IPR011538, InterPro:IN-FAMILY:IPR012336, InterPro:IN-FAMILY:IPR017896, InterPro:IN-FAMILY:IPR017900, InterPro:IN-FAMILY:IPR019554, InterPro:IN-FAMILY:IPR019575, Pfam:IN-FAMILY:PF00037, Pfam:IN-FAMILY:PF01512, Pfam:IN-FAMILY:PF10531, Pfam:IN-FAMILY:PF10589, Prosite:IN-FAMILY:PS00198, Prosite:IN-FAMILY:PS00645, Prosite:IN-FAMILY:PS51379, Smart:IN-FAMILY:SM00928

This subunit contains three 4Fe-4S cluster and one 2Fe-2S cluster, FMN and NAD binding sites.

Citations: [Verhagen99, Schut09]

Subunit of bifurcating [FeFe]-hydrogenase (soluble): hydrogenase γ subunit

Synonyms: HydC

Gene: hydC Accession Number: G-237 (MetaCyc)

Locations: cytosol

Molecular Weight: 18.025 kD (from nucleotide sequence)

GO Terms:
Cellular Component:
GO:0005829 - cytosol []

Unification Links: Protein Model Portal:O52681, UniProt:O52681

Relationship Links: InterPro:IN-FAMILY:IPR002023, InterPro:IN-FAMILY:IPR012336, Panther:IN-FAMILY:PTHR10371, Pfam:IN-FAMILY:PF01257, Prosite:IN-FAMILY:PS01099

This subunit contains one [2Fe2S] cluster and is involved in electron transfer and substrate recognition.

Citations: [Verhagen99, Schut09]


Happe93: Happe T, Naber JD (1993). "Isolation, characterization and N-terminal amino acid sequence of hydrogenase from the green alga Chlamydomonas reinhardtii." Eur J Biochem 214(2);475-81. PMID: 8513797

Herrmann08: Herrmann G, Jayamani E, Mai G, Buckel W (2008). "Energy conservation via electron-transferring flavoprotein in anaerobic bacteria." J Bacteriol 190(3);784-91. PMID: 18039764

Juszczak91: Juszczak A, Aono S, Adams MW (1991). "The extremely thermophilic eubacterium, Thermotoga maritima, contains a novel iron-hydrogenase whose cellular activity is dependent upon tungsten." J Biol Chem 1991;266(21);13834-41. PMID: 1649830

Park06: Park YJ, Yoo CB, Choi SY, Lee HB (2006). "Purifications and characterizations of a ferredoxin and its related 2-oxoacid:ferredoxin oxidoreductase from the hyperthermophilic archaeon, Sulfolobus solfataricus P1." J Biochem Mol Biol 39(1);46-54. PMID: 16466637

Posewitz04a: Posewitz MC, King PW, Smolinski SL, Zhang L, Seibert M, Ghirardi ML (2004). "Discovery of two novel radical S-adenosylmethionine proteins required for the assembly of an active [Fe] hydrogenase." J Biol Chem 279(24);25711-20. PMID: 15082711

Schut09: Schut GJ, Adams MW (2009). "The iron-hydrogenase of Thermotoga maritima utilizes ferredoxin and NADH synergistically: a new perspective on anaerobic hydrogen production." J Bacteriol 191(13);4451-7. PMID: 19411328

Sun10: Sun J, Hopkins RC, Jenney FE, McTernan PM, Adams MW (2010). "Heterologous expression and maturation of an NADP-dependent [NiFe]-hydrogenase: a key enzyme in biofuel production." PLoS One 5(5);e10526. PMID: 20463892

Verhagen99: Verhagen MF, O'Rourke T, Adams MW (1999). "The hyperthermophilic bacterium, Thermotoga maritima, contains an unusually complex iron-hydrogenase: amino acid sequence analyses versus biochemical characterization." Biochim Biophys Acta 1999;1412(3);212-29. PMID: 10482784

Vignais08: Vignais PM (2008). "Hydrogenases and H(+)-reduction in primary energy conservation." Results Probl Cell Differ 45;223-52. PMID: 18500479

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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