[NiFe] Group 3a-hydrogenase
This entry was last updated at: Feb. 9, 2018, 7:13 a.m.
Properties
| Group | [NiFe] Group 3: Cofactor-coupled bidirectional [NiFe] hydrogenases |
| Subgroup | [NiFe] Group 3a: F420-coupled |
| Function | Directly couples oxidation of H2 to reduction of F420 during hydrogenotrophic methanogenesis. Reverse reaction proposed to occur during methylotrophic methanogenesis. Electrons flow between H2-activating hydrogenase subunits to F420 reductase subunit. |
| Activity | Bidirectional |
| Oxygen tolerance | O2-tolerant |
| Localisation | Cytosolic |
Distribution
| Ecosystem distribution | Methanogenic environments such as anoxic soils, marine sediments, and gastrointestinal tracts |
| Taxonomic distribution | Encoded in all hydrogenotrophic methanogens |
Genetic Organisation
e.g. Methanothermobacter marburgensis (WP_013296467.1):
Architecture
| Structures |
|
| Subunits | 3 |
| Subunit description | FrhA (hydrogenase large subunit) FrhG (hydrogenase small subunit) FrhB (F420 reductase subunit) |
| Catalytic site | [NiFe]-centre or [NiFeSe]-centre |
| FeS clusters | Proximal: 4Cys[4Fe4S] or 3Cys1Asp[4Fe4S] |
Important Notes
This subgroup also includes a small lineage of enzymes in Thermococci. As this order does not synthesize F420, these hydrogenases presumably couple H2 oxidation to the reduction of another flavin or nicotinamide compound.
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_015286660.1 | Methanoregula formicica | [NiFe] Group 3a | Euryarchaeota | Methanomicrobiales | Anaerobic Uptake | Sensitive | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | F420 reductase |
| WP_015733355.1 | Methanocaldococcus vulcanius | [NiFe] Group 3a | Euryarchaeota | Methanococcales | Anaerobic Uptake | Sensitive | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | F420 reductase |
| WP_015791787.1 | Methanocaldococcus fervens | [NiFe] Group 3a | Euryarchaeota | Methanococcales | Anaerobic Uptake | Sensitive | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | F420 reductase |
| WP_015857693.1 | Thermococcus gammatolerans | [NiFe] Group 3a | Euryarchaeota | Thermococcales | Anaerobic Uptake | Sensitive | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | F420 reductase |
| WP_016359193.1 | Methanobrevibacter sp. AbM4 | [NiFe] Group 3a | Euryarchaeota | Methanobacteriales | Anaerobic Uptake | Sensitive | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | F420 reductase |
| WP_018154259.1 | Methanothermococcus thermolithotrophicus | [NiFe] Group 3a | Euryarchaeota | Methanococcales | Anaerobic Uptake | Sensitive | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | F420 reductase |
| WP_018154655.1 | Methanothermococcus thermolithotrophicus | [NiFe] Group 3a | Euryarchaeota | Methanococcales | Anaerobic Uptake | Sensitive | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | F420 reductase |
| WP_019262624.1 | Methanobrevibacter smithii | [NiFe] Group 3a | Euryarchaeota | Methanobacteriales | Anaerobic Uptake | Sensitive | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | F420 reductase |
| WP_022846160.1 | Desulfurobacterium sp. TC5-1 | [NiFe] Group 3a | Aquificae | Desulfurobacteriales | Anaerobic Uptake | Sensitive | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | F420 reductase |
| WP_023993015.1 | Methanobacterium sp. MB1 | [NiFe] Group 3a | Euryarchaeota | Methanobacteriales | Anaerobic Uptake | Sensitive | 3 | [NiFe]-centre, 3 x [4Fe4S] clusters | F420 reductase |
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.
- 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.
- Lee, S.H., Kim, M.S., Kim, Y.J., Kim, T.W., Kang, S.G., and Lee, H.S., 2017. Transcriptomic profiling and its implications for the H2 production of a non-methanogen deficient in the frhAGB-encoding hydrogenase. Appl. Microbiol. Biotechnol. 101: 5081-5088.
- Noll, I., Müller, S., and Klein, A. (1999) Transcriptional regulation of genes encoding the selenium-free [NiFe]-hydrogenases in the archaeon Methanococcus voltae involves positive and negative control elements. Genet. 152: 1335-1341.
- Vignais, P.M., Billoud, B., and Meyer, J. (2001) Classification and phylogeny of hydrogenases. FEMS Microbiol. Rev. 25: 455-501.
Physiology:
- Baron, S.F., Brown, D.P., and Ferry, J.G. (1987) Locations of the hydrogenases of Methanobacterium formicicum after subcellular fractionation of cell extract. J. Bacteriol. 169 3823-3825.
- de Poorter, L.M.I., Geerts, W.J., and Keltjens, J.T. (2005) Hydrogen concentrations in methane-forming cells probed by the ratios of reduced and oxidized coenzyme F420. Microbiol. 151: 1697-1705.
- Hendrickson, E.L. and Leigh, J. (2008) Roles of coenzyme F420-reducing hydrogenases and hydrogen- and F420-dependent methylenetetrahydromethanopterin dehydrogenases in reduction of F420 and production of hydrogen during methanogenesis. J. Bacteriol. 190: 4818-4821.
- Kulkarni, G., Kridelbaugh, D.M., Guss, A.M., and Metcalf, W.W. (2009) Hydrogen is a preferred intermediate in the energy-conserving electron transport chain of Methanosarcina barkeri. Proc. Natl. Acad. Sci. USA 106: 15915-15920.
- Jeon, J.H., et al. (2014) Characterization of the frhAGB-encoding hydrogenase from a non-methanogenic hyperthermophilic archaeon. Extremophiles 19: 109-118.
- Lünsdorf, H., Niedrig, M., and Fiebig, K. (1991) Immunocytochemical localization of the coenzyme F420-reducing hydrogenase in Methanosarcina barkeri Fusaro. J. Bacteriol. 173: 978-984.
- Sorgenfrei, O., Müller, S., Pfeiffer, M., Sniezko, I., and Klein, A. (1997) The [NiFe] hydrogenases of Methanococcus voltae: Genes, enzymes and regulation. Arch. Microbiol. 167: 189-195.
- Tzeng, S.F., Wolfe, R.S., and Bryant, M.P. (1975) Factor 420-dependent pyridine nucleotide-linked hydrogenase system of Methanobacterium ruminantium. J. Bacteriol. 121: 184-191.
- Vaupel, M. and Thauer, R.K. (1998) Two F420-reducing hydrogenases in Methanosarcina barkeri. Arch. Microbiol. 169: 201-205.
Biochemistry:
- Allegretti, M., Mills, D.J., McMullan, G., Kühlbrandt, W., and Vonck, J. (2014) Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector. eLife 3: e01963.
- Baron, S.F. and Ferry, J.G. (1989) Purification and properties of the membrane-associated coenzyme F420-reducing hydrogenase from Methanobacterium formicicum. J. Bacteriol. 171: 3846-3853.
- 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.
- Fiebig, K. and Friedrich, B. (1989) Purification of the F420-reducing hydrogenase from Methanosarcina barkeri (strain Fusaro). Eur. J. Biochem. 184: 79-88.
- Greening, C., Ahmed, H.F., Mohamed, E.A., Lee, B.M., Pandey, G., Warden, A., Oakeshott, J.G., Taylor, M.C., and Jackson, C.J. (2016) Physiology, biochemistry, and applications of F420 and Fo dependent redox reactions. Microbiol. Mol. Biol. Rev. 80: 451-493.
- Jacobson, F.S., Daniels, L., Fox, J.A., Walsh, C.T., and Orme-Johnson, W.H. (1982) Purification and properties of an 8-hydroxy-5-deazaflavin-reducing hydrogenase from Methanobacterium thermoautotrophicum. J. Biol. Chem. 257: 3385-3388.
- Mills, D.J., Vitt, S., Strauss, M., Shima, S., and Vonck, J. (2013) De novo modeling of the F420-reducing [NiFe]-hydrogenase from a methanogenic archaeon by cryo-electron microscopy. eLife 2: e00218.
- Muth, E., Mörschel, E., and Klein, A. (1987) Purification and characterization of an 8-hydroxy-5-deazaflavin-reducing hydrogenase from the archaebacterium Methanococcus voltae. Eur. J. Biochem. 169: 571-577.
- Vitt, S., Ma, K., Warkentin, E., Moll, J., Pierik, A.J., Shima, S., and Ermler, U. (2014) The F420-reducing [NiFe]-hydrogenase complex from Methanothermobacter marburgensis, the first X-ray structure of a group 3 family member. J. Mol. Biol. 426: 2813-26.
- Walsh, C.T., Fox, J.A., Livingston, D.J., and Orme-Johnson, W.H. (1987) 8-Hydroxy-5-deazaflavin-reducing hydrogenase from Methanobacterium thermoautotrophicum: 1. Purification and characterization. Biochem. 26: 4219-4227.
- Yamazaki, S. (1982) A selenium-containing hydrogenase from Methanococcus vannielii. Identification of the selenium moiety as a selenocysteine residue. J. Biol. Chem. 257: 7926-7929.
- Yamazaki, S., Tsai, L., Stadtman, T.C., Teshima, T., Nakaji, A., and Shiba, T. (1985) Stereochemical studies of a selenium-containing hydrogenase from Methanococcus vannielii: determination of the absolute configuration of C-5 chirally labeled dihydro-8-hydroxy-5-deazaflavin cofactor. Proc. Natl. Acad. Sci. USA 82: 1364-1366.
Chemistry:
- Kojima, N., Fox, J.A., Hausinger, R.P., Daniels, L., Orme-Johnson, W.H., and Walsh, C. (1983) Paramagnetic centers in the nickel-containing, deazaflavin-reducing hydrogenase from Methanobacterium thermoautotrophicum. Proc. Natl. Acad. Sci. USA 80: 378-382.
- Lindahl, P.A., Kojima, N., Hausinger, R.P., Fox, J.A., Teo, B.K., Walsh, C.T., and Orme-Johnson, W.H. (1984) Nickel and iron EXAFS of F420-reducing hydrogenase from Methanobacterium thermoautotrophicum. J. Am. Chem. Soc. 106: 3062-3064.
- Livingston, D.J., Fox, J.A., Orme-Johnson, W.H., and Walsh, C.T. (1987) 8-hydroxy-5-deazaflavin-reducing hydrogenase from Methanobacterium thermoautotrophicum: 2. Kinetic and hydrogen-transfer studies. Derivation of a steady-state rate equation for deazaflavin-reducing hydrogenase. Biochem. 26: 4228-4237.
- Sorgenfrei, O., Duin, E.C., Klein, A., and Albracht, S.P. (1997) Changes in the electronic structure around Ni in oxidized and reduced selenium-containing hydrogenases from Methanococcus voltae. Eur. J. Biochem. 247: 681-687.