[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_029966039.1	Desulfonauticus sp. A7A	[NiFe] Group 3c	Deltaproteobacteria	Desulfovibrionales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_029898901.1	Desulfovibrio sp. L21-Syr-AB	[NiFe] Group 3c	Deltaproteobacteria	Desulfovibrionales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_028894885.1	Syntrophorhabdus aromaticivorans	[NiFe] Group 3c	Deltaproteobacteria	Syntrophobacterales	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_028584591.1	Desulfobulbus mediterraneus	[NiFe] Group 3c	Deltaproteobacteria	Desulfobacterales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_028583859.1	Desulfobulbus mediterraneus	[NiFe] Group 3c	Deltaproteobacteria	Desulfobacterales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_028580885.1	Desulfobulbus japonicus	[NiFe] Group 3c	Deltaproteobacteria	Desulfobacterales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_028580860.1	Desulfobulbus japonicus	[NiFe] Group 3c	Deltaproteobacteria	Desulfobacterales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_028574551.1	Desulfonatronovibrio hydrogenovorans	[NiFe] Group 3c	Deltaproteobacteria	Desulfovibrionales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_028574115.1	Desulfonatronovibrio hydrogenovorans	[NiFe] Group 3c	Deltaproteobacteria	Desulfovibrionales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_028318776.1	Desulfobulbus elongatus	[NiFe] Group 3c	Deltaproteobacteria	Desulfobacterales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_028317553.1	Desulfobulbus elongatus	[NiFe] Group 3c	Deltaproteobacteria	Desulfobacterales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_027371047.1	Desulfovermiculus halophilus	[NiFe] Group 3c	Deltaproteobacteria	Desulfovibrionales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_027368703.1	Desulfovibrio africanus	[NiFe] Group 3c	Deltaproteobacteria	Desulfovibrionales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_027358538.1	Desulforegula conservatrix	[NiFe] Group 3c	Deltaproteobacteria	Desulfuromonadales	Bidirectional	Tolerant	4	[NiFe]-centre, 1 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_027191993.1	Desulfovibrio putealis	[NiFe] Group 3c	Deltaproteobacteria	Desulfovibrionales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_027187949.1	Desulfovibrio cuneatus	[NiFe] Group 3c	Deltaproteobacteria	Desulfovibrionales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_027183464.1	Desulfovibrio inopinatus	[NiFe] Group 3c	Deltaproteobacteria	Desulfovibrionales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_026167551.1	Desulfovibrio oxyclinae	[NiFe] Group 3c	Deltaproteobacteria	Desulfovibrionales	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_023992472.1	Methanobacterium sp. MB1	[NiFe] Group 3c	Euryarchaeota	Methanobacteriales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_023408290.1	Desulfofustis sp. PB-SRB1	[NiFe] Group 3c	Deltaproteobacteria	Desulfobacterales	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_022775381.1	Symbiobacter mobilis	[NiFe] Group 3c	Betaproteobacteria	Burkholderiales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_022668938.1	Desulfospira joergensenii	[NiFe] Group 3c	Deltaproteobacteria	Desulfobacterales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_022532976.1	Methanoculleus sp. CAG:1088	[NiFe] Group 3c	Euryarchaeota	Methanomicrobiales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_020882283.1	Desulfovibrio sp. X2	[NiFe] Group 3c	Deltaproteobacteria	Desulfovibrionales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_020448391.1	Methanomassiliicoccus intestinalis	[NiFe] Group 3c	Euryarchaeota	Methanomicrobiales	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_019177457.1	Methanomassiliicoccus luminyensis	[NiFe] Group 3c	Euryarchaeota	Methanomicrobiales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_018154262.1	Methanothermococcus thermolithotrophicus	[NiFe] Group 3c	Euryarchaeota	Methanococcales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_018154225.1	Methanothermococcus thermolithotrophicus	[NiFe] Group 3c	Euryarchaeota	Methanococcales	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_015935331.1	Anaeromyxobacter dehalogenans	[NiFe] Group 3c	Deltaproteobacteria	Myxococcales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_015903075.1	Desulfobacterium autotrophicum	[NiFe] Group 3c	Deltaproteobacteria	Desulfobacterales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_015839165.1	Geobacter sp. M21	[NiFe] Group 3c	Deltaproteobacteria	Desulfuromonadales	Bidirectional	Tolerant	4	[NiFe]-centre, 1 x [4Fe4S] clusters	Diaphorase, [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_015752683.1	Desulfohalobium retbaense	[NiFe] Group 3c	Deltaproteobacteria	Desulfovibrionales	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_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_015724435.1	Desulfobulbus propionicus	[NiFe] Group 3c	Deltaproteobacteria	Desulfobacterales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_015722755.1	Desulfobulbus propionicus	[NiFe] Group 3c	Deltaproteobacteria	Desulfobacterales	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_015590675.1	Archaeoglobus sulfaticallidus	[NiFe] Group 3c	Euryarchaeota	Archaeoglobales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_015504206.1	Methanomethylophilus alvus	[NiFe] Group 3c	Euryarchaeota	Unclassified	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_014867732.1	Methanoculleus bourgensis	[NiFe] Group 3c	Euryarchaeota	Methanomicrobiales	Bifurcating	Sensitive	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Polyferredoxin, [FeS] protein
WP_014551809.1	Geobacter sulfurreducens	[NiFe] Group 3c	Deltaproteobacteria	Desulfuromonadales	Bidirectional	Tolerant	4	[NiFe]-centre, 1 x [4Fe4S] clusters	Diaphorase, [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.