[NiFe] Group 4b-hydrogenase

This entry was last updated at: Feb. 9, 2018, 6:24 a.m.

Properties

Group	[NiFe] Group 4: Respiratory H₂-evolving [NiFe] hydrogenases
Subgroup	[NiFe] Group 4b: Formate-respiring
Function	Forms respiratory supercomplex that couples oxidation of low-potential carbon compounds to reduction of protons concomitant with Na⁺ translocation. Electron-input modules include formate dehydrogenases, carbon monoxide dehydrogenases, and potentially glutamate synthases. Electrons flow through hydrogenase resulting in proton reduction to H₂. The energy released is used to translocate Na⁺ ions through Mrp-like antiporter subunits to generate a sodium-motive force.
Activity	H₂-evolution
Oxygen tolerance	O₂-sensitive
Localisation	Membrane-bound

Distribution

Ecosystem distribution	Hydrothermal systems, other high temperature environments
Taxonomic distribution	Encoded in Thermococci, Thermoprotei, and Thermodesulfovibrio

Genetic Organisation

e.g. Pyrococcus abyssi (WP_010868591.1):

Architecture

Structures	None
Subunits	13+
Subunit description	MchD (hydrogenase large subunit) MchF (hydrogenase small subunit) MchC (NuoH-like transmembrane adaptor) MchAB (NuoL-like transmembrane adaptors) MchE (NuoC-like transmembrane adaptor) MchHIJKLMN (Mrp-like antiporter subunits) Form functional complexes with formate dehydrogenases, carbon monoxide dehydrogenases, and glutamate synthases
Catalytic site	[NiFe]-centre
FeS clusters	Proximal: 4Cys[4Fe4S] Medial: Absent Distal: Absent

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_011388069.1	Rhodospirillum rubrum	[NiFe] Group 4b	Alphaproteobacteria	Rhodospirillales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_028450152.1	Chitinibacter tainanensis	[NiFe] Group 4b	Betaproteobacteria	Neisseriales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_028451288.1	Chitinilyticum aquatile	[NiFe] Group 4b	Betaproteobacteria	Neisseriales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_026263170.1	Chitiniphilus shinanonensis	[NiFe] Group 4b	Betaproteobacteria	Neisseriales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_014767907.1	Desulfurococcus fermentans	[NiFe] Group 4b	Crenarchaeota	Desulfurococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_012608688.1	Desulfurococcus kamchatkensis	[NiFe] Group 4b	Crenarchaeota	Desulfurococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_013561596.1	Desulfurococcus mucosus	[NiFe] Group 4b	Crenarchaeota	Desulfurococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_011839350.1	Staphylothermus marinus	[NiFe] Group 4b	Crenarchaeota	Desulfurococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_014737671.1	Thermogladius cellulolyticus	[NiFe] Group 4b	Crenarchaeota	Desulfurococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_013128928.1	Thermosphaera aggregans	[NiFe] Group 4b	Crenarchaeota	Desulfurococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_010868591.1	Pyrococcus abyssi	[NiFe] Group 4b	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_013905846.1	Pyrococcus yayanosii	[NiFe] Group 4b	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_013467422.1	Thermococcus barophilus	[NiFe] Group 4b	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_015857865.1	Thermococcus gammatolerans	[NiFe] Group 4b	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_015857684.1	Thermococcus gammatolerans	[NiFe] Group 4b	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_004068373.1	Thermococcus litoralis	[NiFe] Group 4b	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_012571234.1	Thermococcus onnurineus	[NiFe] Group 4b	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_012571983.1	Thermococcus onnurineus	[NiFe] Group 4b	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_012572531.1	Thermococcus onnurineus	[NiFe] Group 4b	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_014012072.1	Thermococcus sp. 4557	[NiFe] Group 4b	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_014123101.1	Thermococcus sp. AM4	[NiFe] Group 4b	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_014122941.1	Thermococcus sp. AM4	[NiFe] Group 4b	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_020505780.1	Lamprocystis purpurea	[NiFe] Group 4b	Gammaproteobacteria	Chromatiales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_028842781.1	Thermodesulfovibrio islandicus	[NiFe] Group 4b	Nitrospirae	Nitrospirales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_028845048.1	Thermodesulfovibrio thiophilus	[NiFe] Group 4b	Nitrospirae	Nitrospirales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_012545774.1	Thermodesulfovibrio yellowstonii	[NiFe] Group 4b	Nitrospirae	Nitrospirales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.

Literature

Genetics:

Kim, M.S., Bae, S.S., Kim, Y.J., Kim, T.W., Lim, J.K., Lee, S.H., Choi, A.R., Jeon, J.H., Lee, J.H., Lee, H.S., and Kang, S.G. (2013) CO-dependent H₂ production by genetically engineered Thermococcus onnurineus NA1. Appl. Environ. Microbiol. 79: 2048-2053.
Lee, S.H., Kim, M.S., Bae, S.S., Choi, A.R., Lee, J.W., Kim, T.W., Lee, J.H., Lee, H.S., and Kang, S.G. (2014) Comparison of CO-dependent H₂ production with strong promoters in Thermococcus onnurineus NA1. Appl. Microbiol. Biotechnol. 98: 979-986.
Lim, J.K., Kang, S.G., Lebedinsky, A.V., Lee, J.H., and Lee, H.S. (2010) Identification of a novel class of membrane-bound [NiFe]-hydrogenases in Thermococcus onnurineus NA1 by in silico analysis. Appl. Environ. Microbiol. 76: 6286-6289.
Lipscomb, G.L., Schut, G.J., Thorgersen, M.P., Nixon, W.J., Kelly, R.M. and Adams, M.W. (2014) Engineering hydrogen gas production from formate in a hyperthermophile by heterologous production of an 18-subunit membrane-bound complex. J. Biol. Chem. 289: 2873-2879.
Moon, Y.J., Kwon, J., Yun, S.H., Lim, H.L., Kim, M.S., Kang, S.G., Lee, J.H., Choi, J.S., Kim, S.I., and Chung, Y.H. (2012) Proteome analyses of hydrogen-producing hyperthermophilic archaeon Thermococcus onnurineus NA1 in different one-carbon substrate culture conditions. Mol. Cell. Proteomics 11: M111-015420.
Schut, G.J., Lipscomb, G.L., Nguyen, D.M., Kelly, R.M., and Adams, M.W. (2016) Heterologous production of an energy-conserving carbon monoxide dehydrogenase complex in the hyperthermophile Pyrococcus furiosus. Front. Microbiol. 7: In press.
Søndergaard, D., Petersen, C.N.S., and Greening, C. (2017) HydDB: a web tool for hydrogenase classification and analysis. Sci. Rep. 6: 34212.
Takács, M., Tóth, A., Bogos, B., Varga, A., Rákhely, G., and Kovács, K.L. (2008) Formate hydrogenlyase in the hyperthermophilic archaeon, Thermococcus litoralis. BMC Microbiol. 8: 88.
Yun, S.H., Kwon, S.O., Park, G.W., Kim, J.Y., Kang, S.G., Lee, J.H., Chung, Y.H., Kim, S., Choi, J.S., and Kim, S.I. (2011) Proteome analysis of Thermococcus onnurineus NA1 reveals the expression of hydrogen gene cluster under carboxydotrophic growth. J. Proteomics 74: 1926-1933.

Physiology:

Bae, S.S., Kim, T.W., Lee, H.S., Kwon, K.K., Kim, Y.J., Kim, M.S., Lee, J.H., and Kang, S.G. (2012) H₂ production from CO, formate or starch using the hyperthermophilic archaeon, Thermococcus onnurineus. Biotechnol. Lett. 34: 75-79.
Bae, S.S., Lee, H.S., Jeon, J.H., Lee, J.H., Kang, S.G. and Kim, T.W. (2015) Enhancing bio-hydrogen production from sodium formate by hyperthermophilic archaeon, Thermococcus onnurineus NA1. Bioproc. Biosyst. Eng. 38: 989-993.
Kim, Y.J. et al. (2010). Formate-driven growth coupled with H₂ production. Nature 467: 352-355.
Lim, J.K., Bae, S.S., Kim, T.W., Lee, J.H., Lee, H.S., and Kang, S.G. (2012) Thermodynamics of formate-oxidizing metabolism and implications for H₂ production. Appl. Environ. Microbiol. 78: 7393-7397.
Lim, J.K., Mayer, F., Kang, S.G. and Müller, V. (2014) Energy conservation by oxidation of formate to carbon dioxide and hydrogen via a sodium ion current in a hyperthermophilic archaeon. Proc. Natl. Acad. Sci. USA 111: 11497-11502.
Schut, G.J., Boyd, E.S., Peters, J.W., and Adams, M.W. (2013) The modular respiratory complexes involved in hydrogen and sulfur metabolism by heterotrophic hyperthermophilic archaea and their evolutionary implications. FEMS Microbiol. Rev. 37: 182-203.