[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 |
|
| 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) |
|---|---|---|---|---|---|---|---|---|---|
| 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_004031311.1 | Methanobacterium formicicum | [NiFe] Group 3c | Euryarchaeota | Methanobacteriales | 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_004039570.1 | Methanofollis liminatans | [NiFe] Group 3c | Euryarchaeota | Methanomicrobiales | Bifurcating | Sensitive | 4 | [NiFe]-centre, 3 x [4Fe4S] clusters | Polyferredoxin, [FeS] protein |
| WP_004512544.1 | Geobacter metallireducens | [NiFe] Group 3c | Deltaproteobacteria | Desulfuromonadales | Bidirectional | Tolerant | 4 | [NiFe]-centre, 1 x [4Fe4S] clusters | Diaphorase, [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_006930005.1 | Caldithrix abyssi | [NiFe] Group 3c | Caldithrix | Caldithrixales | Bifurcating | Sensitive | 4 | [NiFe]-centre, 3 x [4Fe4S] clusters | Polyferredoxin, [FeS] protein |
| WP_007043614.1 | Methanotorris formicicus | [NiFe] Group 3c | Euryarchaeota | Methanococcales | Bifurcating | Sensitive | 4 | [NiFe]-centre, 3 x [4Fe4S] clusters | Polyferredoxin, [FeS] protein |
| WP_007044701.1 | Methanotorris formicicus | [NiFe] Group 3c | Euryarchaeota | Methanococcales | Bifurcating | Sensitive | 4 | [NiFe]-centre, 3 x [4Fe4S] clusters | Polyferredoxin, [FeS] protein |
| WP_008869690.1 | Desulfonatronospira thiodismutans | [NiFe] Group 3c | Deltaproteobacteria | Desulfovibrionales | Bifurcating | Sensitive | 4 | [NiFe]-centre, 3 x [4Fe4S] clusters | Polyferredoxin, [FeS] protein |
| WP_008870928.1 | Desulfonatronospira thiodismutans | [NiFe] Group 3c | Deltaproteobacteria | Desulfovibrionales | 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_010876758.1 | Methanothermobacter thermoautotrophicus | [NiFe] Group 3c | Euryarchaeota | Methanobacteriales | 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_010936390.1 | Dehalococcoides mccartyi | [NiFe] Group 3c | Chloroflexi | Dehalococcoidales | Bifurcating | Sensitive | 4 | [NiFe]-centre, 3 x [4Fe4S] clusters | Polyferredoxin, [FeS] protein |
| WP_011018550.1 | Methanopyrus kandleri | [NiFe] Group 3c | Euryarchaeota | Methanopyrales | Bifurcating | Sensitive | 4 | [NiFe]-centre, 3 x [4Fe4S] clusters | Polyferredoxin, [FeS] protein |
| WP_011018638.1 | Methanopyrus kandleri | [NiFe] Group 3c | Euryarchaeota | Methanopyrales | 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 |
| WP_011188256.1 | Desulfotalea psychrophila | [NiFe] Group 3c | Deltaproteobacteria | Desulfobacterales | 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_011698648.1 | Syntrophobacter fumaroxidans | [NiFe] Group 3c | Deltaproteobacteria | Syntrophobacterales | Bifurcating | Sensitive | 4 | [NiFe]-centre, 3 x [4Fe4S] clusters | Polyferredoxin, [FeS] protein |
| WP_011699072.1 | Syntrophobacter fumaroxidans | [NiFe] Group 3c | Deltaproteobacteria | Syntrophobacterales | Bifurcating | Sensitive | 4 | [NiFe]-centre, 3 x [4Fe4S] clusters | Polyferredoxin, [FeS] protein |
| WP_011700332.1 | Syntrophobacter fumaroxidans | [NiFe] Group 3c | Deltaproteobacteria | Syntrophobacterales | Bifurcating | Sensitive | 4 | [NiFe]-centre, 3 x [4Fe4S] clusters | Polyferredoxin, [FeS] protein |
| WP_011700738.1 | Syntrophobacter fumaroxidans | [NiFe] Group 3c | Deltaproteobacteria | Syntrophobacterales | Bifurcating | Sensitive | 4 | [NiFe]-centre, 3 x [4Fe4S] clusters | Polyferredoxin, [FeS] protein |
| WP_011843851.1 | Methanoculleus marisnigri | [NiFe] Group 3c | Euryarchaeota | Methanomicrobiales | Bifurcating | Sensitive | 4 | [NiFe]-centre, 3 x [4Fe4S] clusters | Polyferredoxin, [FeS] protein |
| WP_011971888.1 | Methanococcus vannielii | [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_011973924.1 | Methanococcus aeolicus | [NiFe] Group 3c | Euryarchaeota | Methanococcales | 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_012036601.1 | Methanocella arvoryzae | [NiFe] Group 3c | Euryarchaeota | Methanocellales | Bifurcating | Sensitive | 4 | [NiFe]-centre, 3 x [4Fe4S] clusters | Polyferredoxin, [FeS] protein |
| WP_012065828.1 | Methanococcus vannielii | [NiFe] Group 3c | Euryarchaeota | Methanococcales | Bifurcating | Sensitive | 4 | [NiFe]-centre, 3 x [4Fe4S] clusters | Polyferredoxin, [FeS] protein |
| WP_012099129.1 | Anaeromyxobacter sp. Fw109-5 | [NiFe] Group 3c | Deltaproteobacteria | Myxococcales | 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_012309762.1 | Korarchaeum cryptofilum | [NiFe] Group 3c | Korarchaeota | Unclassified | Bifurcating | Sensitive | 4 | [NiFe]-centre, 3 x [4Fe4S] clusters | Polyferredoxin, [FeS] protein |
| WP_012376486.1 | Opitutus terrae | [NiFe] Group 3c | Verrucomicrobia | Opitutales | Bifurcating | Sensitive | 4 | [NiFe]-centre, 3 x [4Fe4S] clusters | Polyferredoxin, [FeS] protein |
| WP_012469611.1 | Geobacter lovleyi | [NiFe] Group 3c | Deltaproteobacteria | Desulfuromonadales | Bidirectional | Tolerant | 4 | [NiFe]-centre, 1 x [4Fe4S] clusters | Diaphorase, [FeS] protein |
| WP_012528247.1 | Anaeromyxobacter sp. K | [NiFe] Group 3c | Deltaproteobacteria | Myxococcales | Bifurcating | Sensitive | 4 | [NiFe]-centre, 3 x [4Fe4S] clusters | Polyferredoxin, [FeS] protein |
| WP_012532312.1 | Geobacter bemidjiensis | [NiFe] Group 3c | Deltaproteobacteria | Desulfuromonadales | Bidirectional | Tolerant | 4 | [NiFe]-centre, 1 x [4Fe4S] clusters | Diaphorase, [FeS] protein |
| WP_012545782.1 | Thermodesulfovibrio yellowstonii | [NiFe] Group 3c | Nitrospirae | Nitrospirales | 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_012956704.1 | Methanobrevibacter ruminantium | [NiFe] Group 3c | Euryarchaeota | Methanobacteriales | 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_012979819.1 | Methanocaldococcus sp. FS406-22 | [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_013099800.1 | Methanocaldococcus infernus | [NiFe] Group 3c | Euryarchaeota | Methanococcales | Bifurcating | Sensitive | 4 | [NiFe]-centre, 3 x [4Fe4S] clusters | Polyferredoxin, [FeS] protein |
| WP_013179971.1 | Methanococcus voltae | [NiFe] Group 3c | Euryarchaeota | Methanococcales | Bifurcating | Sensitive | 4 | [NiFe]-centre, 3 x [4Fe4S] clusters | Polyferredoxin, [FeS] protein |
| WP_013180651.1 | Methanococcus voltae | [NiFe] Group 3c | Euryarchaeota | Methanococcales | Bifurcating | Sensitive | 4 | [NiFe]-centre, 3 x [4Fe4S] clusters | Polyferredoxin, [FeS] protein |
| WP_013218178.1 | Dehalogenimonas lykanthroporepellens | [NiFe] Group 3c | Chloroflexi | Dehalogenimonas | 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.