[NiFe] Group 3c-hydrogenase

This entry was last updated at: June 13, 2016, 11:23 a.m.

Properties

Group	[NiFe] Group 3: Cofactor-coupled bidirectional [NiFe] hydrogenases
Subgroup	[NiFe] Group 3c: Heterodisulfide reductase-linked
Function	Bifurcates electrons from H₂ to heterodisulfide and ferredoxin. This is the final step in the Wolfe cycle of methanogenesis.
Activity	Electron-bifurcation
Oxygen tolerance	O₂-tolerant?
Localisation	Cytosolic

Distribution

Ecosystem distribution	Methanogenic environments such as anoxic soils, marine sediments, and gastrointestinal tracts
Taxonomic distribution	Encoded in most methanogens and sulfate-reducing bacteria

Genetic Organisation

e.g. Methanothermobacter marburgensis (WP_013296307.1):

Architecture

Structures	None
Subunits	4
Subunit description	MvhA (hydrogenase large subunit) MvhG (hydrogenase small subunit) MvhD (iron-sulfur subunit) MvhB (polyferredoxin subunit) Forms complex with heterodisulfide reductase (HdrABC)
Catalytic site	[NiFe]-centre or [NiFeSe]-centre
FeS clusters	Proximal: 4Cys[4Fe4S] Medial: 4Cys[4Fe4S] Distal: 4Cys[4Fe4S]

Sequences in this class

NCBI Accession	Organism	Hydrogenase Class	Phylum	Order	Activity (Predicted)	Oxygen Tolerance (Predicted)	Subunits (Predicted)	Metal Centres (Predicted)	Accessory Subunits (Predicted)
WP_012376486.1	Opitutus terrae	[NiFe] Group 3c	Verrucomicrobia	Opitutales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_022853555.1	Thermodesulfatator atlanticus	[NiFe] Group 3c	Thermodesulfobacteria	Thermodesulfobacteriales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_028840908.1	Thermodesulfobacterium hveragerdense	[NiFe] Group 3c	Thermodesulfobacteria	Thermodesulfobacteriales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_012545782.1	Thermodesulfovibrio yellowstonii	[NiFe] Group 3c	Nitrospirae	Nitrospirales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
KKK40681.1	Lokiarchaeum sp. GC14_75	[NiFe] Group 3c	Lokiarchaeota	N/A	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_012309762.1	Korarchaeum cryptofilum	[NiFe] Group 3c	Korarchaeota	Unclassified	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_012302733.1	Desulforudis audaxviator	[NiFe] Group 3c	Firmicutes	Clostridiales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_015617925.1	Desulfotomaculum gibsoniae	[NiFe] Group 3c	Firmicutes	Clostridiales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_015739967.1	Ammonifex degensii	[NiFe] Group 3c	Firmicutes	Thermoanaerobacterales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_013756665.1	Thermodesulfobium narugense	[NiFe] Group 3c	Firmicutes	Thermoanaerobacterales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_013908379.1	Thermodesulfatator indicus	[NiFe] Group 3c	Firmicutes	Thermodesulfobacteriales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_010878869.1	Archaeoglobus fulgidus	[NiFe] Group 3c	Euryarchaeota	Archaeoglobales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_015590675.1	Archaeoglobus sulfaticallidus	[NiFe] Group 3c	Euryarchaeota	Archaeoglobales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_013684228.1	Archaeoglobus veneficus	[NiFe] Group 3c	Euryarchaeota	Archaeoglobales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_012965352.1	Ferroglobus placidus	[NiFe] Group 3c	Euryarchaeota	Archaeoglobales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_015233716.1	Natronobacterium gregoryi	[NiFe] Group 3c	Euryarchaeota	Halobacteriales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_004032005.1	Methanobacterium formicicum	[NiFe] Group 3c	Euryarchaeota	Methanobacteriales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_004031311.1	Methanobacterium formicicum	[NiFe] Group 3c	Euryarchaeota	Methanobacteriales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_013644241.1	Methanobacterium lacus	[NiFe] Group 3c	Euryarchaeota	Methanobacteriales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_013643973.1	Methanobacterium lacus	[NiFe] Group 3c	Euryarchaeota	Methanobacteriales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_013826546.1	Methanobacterium paludis	[NiFe] Group 3c	Euryarchaeota	Methanobacteriales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_013826227.1	Methanobacterium paludis	[NiFe] Group 3c	Euryarchaeota	Methanobacteriales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_023992472.1	Methanobacterium sp. MB1	[NiFe] Group 3c	Euryarchaeota	Methanobacteriales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_023992781.1	Methanobacterium sp. MB1	[NiFe] Group 3c	Euryarchaeota	Methanobacteriales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_012956704.1	Methanobrevibacter ruminantium	[NiFe] Group 3c	Euryarchaeota	Methanobacteriales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_019264891.1	Methanobrevibacter smithii	[NiFe] Group 3c	Euryarchaeota	Methanobacteriales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_019262575.1	Methanobrevibacter smithii	[NiFe] Group 3c	Euryarchaeota	Methanobacteriales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_016359076.1	Methanobrevibacter sp. AbM4	[NiFe] Group 3c	Euryarchaeota	Methanobacteriales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_011405926.1	Methanosphaera stadtmanae	[NiFe] Group 3c	Euryarchaeota	Methanobacteriales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_013296307.1	Methanothermobacter marburgensis	[NiFe] Group 3c	Euryarchaeota	Methanobacteriales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_010876758.1	Methanothermobacter thermoautotrophicus	[NiFe] Group 3c	Euryarchaeota	Methanobacteriales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_013413806.1	Methanothermus fervidus	[NiFe] Group 3c	Euryarchaeota	Methanobacteriales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_012036601.1	Methanocella arvoryzae	[NiFe] Group 3c	Euryarchaeota	Methanocellales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_012036509.1	Methanocella arvoryzae	[NiFe] Group 3c	Euryarchaeota	Methanocellales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_014407035.1	Methanocella conradii	[NiFe] Group 3c	Euryarchaeota	Methanocellales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_014404721.1	Methanocella conradii	[NiFe] Group 3c	Euryarchaeota	Methanocellales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_012901238.1	Methanocella paludicola	[NiFe] Group 3c	Euryarchaeota	Methanocellales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_012901516.1	Methanocella paludicola	[NiFe] Group 3c	Euryarchaeota	Methanocellales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_015790819.1	Methanocaldococcus fervens	[NiFe] Group 3c	Euryarchaeota	Methanococcales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_013099800.1	Methanocaldococcus infernus	[NiFe] Group 3c	Euryarchaeota	Methanococcales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_010870705.1	Methanocaldococcus jannaschii	[NiFe] Group 3c	Euryarchaeota	Methanococcales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_012980416.1	Methanocaldococcus sp. FS406-22	[NiFe] Group 3c	Euryarchaeota	Methanococcales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_012979819.1	Methanocaldococcus sp. FS406-22	[NiFe] Group 3c	Euryarchaeota	Methanococcales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_004589824.1	Methanocaldococcus villosus	[NiFe] Group 3c	Euryarchaeota	Methanococcales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_015733560.1	Methanocaldococcus vulcanius	[NiFe] Group 3c	Euryarchaeota	Methanococcales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_015732794.1	Methanocaldococcus vulcanius	[NiFe] Group 3c	Euryarchaeota	Methanococcales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_011973924.1	Methanococcus aeolicus	[NiFe] Group 3c	Euryarchaeota	Methanococcales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_011972821.1	Methanococcus aeolicus	[NiFe] Group 3c	Euryarchaeota	Methanococcales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_011170767.1	Methanococcus maripaludis	[NiFe] Group 3c	Euryarchaeota	Methanococcales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_011171638.1	Methanococcus maripaludis	[NiFe] Group 3c	Euryarchaeota	Methanococcales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein

Literature

Genetics:

Berghöfer, Y., Agha-Amiri, K., and Klein, A. (1994) Selenium is involved in the negative regulation of the expression of selenium-free [NiFe] hydrogenases in Methanococcus voltae. Mol. Gen. Genet. 242: 369-373.
Coppi, M.V. (2005) The hydrogenases of Geobacter sulfurreducens: a comparative genomic perspective. Microbiol. 151: 1239-1254.
Mander, G.J., Pierik, A.J., Huber, H., and Hedderich, R. (2004) Two distinct heterodisulfide reductase-like enzymes in the sulfate-reducing archaeon Archaeoglobus profundus. Eur. J. Biochem. 271: 1106-1116.
Halboth, S. and Klein, A. (1992) Methanococcus voltae harbors four gene clusters potentially encoding two [NiFe] and two [NiFeSe] hydrogenases, each of the cofactor F₄₂₀-reducing or F₄₂₀-non-reducing types. Mol. Gen. Genet. 233: 217-224.
Hocking, W.P., Stokke, R., Roalkvam, I., and Steen, I.H. (2014) Identification of key components in the energy metabolism of the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus by transcriptome analyses. Front. Microbiol. 5: 95.
Reeve, J.N., Beckler, G.S., Cram, D.S., Hamilton, P.T., Brown, J.W., Krzycki, J.A., Kolodziej, A.F., Alex, L., Orme-Johnson, W.H., and Walsh, C.T. (1989) A hydrogenase-linked gene in Methanobacterium thermoautotrophicum strain delta H encodes a polyferredoxin. Proc. Natl. Acad. Sci. USA 86: 3031-3035.
Steigerwald, V.J., Beckler, G.S., and Reeve, J.N. (1990) Conservation of hydrogenase and polyferredoxin structures in the hyperthermophilic archaebacterium Methanothermus fervidus. J. Bacteriol. 172: 4715-4718.
Vignais, P.M., Billoud, B., and Meyer, J. (2001) Classification and phylogeny of hydrogenases. FEMS Microbiol. Rev. 25: 455-501.

Physiology:

Costa, K.C., Lie, T.J., Xia, Q., and Leigh, J.A. (2013) VhuD facilitates electron flow from H₂ or formate to heterodisulfide reductase in Methanococcus maripaludis. J. Bacteriol. 195: 5160-5165.
Costa, K.C., Wong, P.M., Wang, T., Lie, T.J., Dodsworth, J.A., Swanson, I., Burn, J.A., Hackett, M., and Leigh, J.A. (2010) Protein complexing in a methanogen suggests electron bifurcation and electron delivery from formate to heterodisulfide reductase. Proc. Natl. Acad. Sci. USA 107: 11050-11055.
Kaster, A.K., Moll, J., Parey, K., and Thauer, R.K. (2011) Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic archaea. Proc. Acad. Natl. Sci. USA 108: 2981-2986.
Kröninger, L., Berger, S., Welte, C., and Deppenmeier, U. (2015) Evidence for the involvement of two heterodisulfide reductases in the energy-conserving system of Methanomassiliicoccus luminyensis. FEBS J.: in press.
Pfeiffer, M., Bestgen, H., Bürger, A., and Klein, A. (1998) The vhuU gene encoding a small subunit of a selenium-containing [NiFe]-hydrogenase in Methanococcus voltae appears to be essential for the cell. Arch. Microbiol. 170: 418-426.
Stojanowic, A., Mander, G.J., Duin, E.C., and Hedderich, R. (2003) Physiological role of the F₄₂₀-non-reducing hydrogenase (Mvh) from Methanothermobacter marburgensis. Arch. Microbiol. 180: 194-203.
Thauer, R.K., 2012. The Wolfe cycle comes full circle. Proc. Acad. Natl. Sci. USA 109: 15084-15085.
Thauer, R.K., Kaster, A.K., Seedorf, H., Buckel, W., and Hedderich, R. (2008) Methanogenic archaea: ecologically relevant differences in energy conservation. Nat. Rev. Microbiol. 6: 579-591.
Woo, G.J., Wasserfallen, A., and Wolfe, R.S. (1993) Methyl viologen hydrogenase II, a new member of the hydrogenase family from Methanobacterium thermoautotrophicum delta H. J. Bacteriol. 175: 5970-5977.

Biochemistry:

Braks, I.J., Hoppert, M., Roge, S., and Mayer, F. (1994) Structural aspects and immunolocalization of the F₄₂₀-reducing and non-F₄₂₀-reducing hydrogenases from Methanobacterium thermoautotrophicum Marburg. J. Bacteriol. 176: 7677-7687.
Setzke, E., Hedderich, R., Heiden, S., and Thauer, R.K. (1994). H₂: heterodisulfide oxidoreductase complex from Methanobacterium thermoautotrophicum. Eur. J. Biochem. 220: 139-148.

Chemistry:

Sorgenfrei, O., Duin, E.C., Klein, A., and Albracht, S.P. (1996) Interactions of ⁷⁷Se and ¹³CO with nickel in the active site of active F₄₂₀-nonreducing hydrogenase from Methanococcus voltae. J. Biol. Chem. 271: 23799-23806.
Sorgenfrei, O., Klein, A. and Albracht, S.P. (1993) Influence of illumination on the electronic interaction between ⁷⁷Se and nickel in active F₄₂₀-non-reducing hydrogenase from Methanococcus voltae. FEBS Lett. 332: 291-297.