[NiFe] Group 3a-hydrogenase

This entry was last updated at: Feb. 9, 2018, 7:13 a.m.

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):

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 F_o 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.