[NiFe] Group 4d-hydrogenase

This entry was last updated at: May 22, 2018, 1:09 a.m.

Properties

Group	[NiFe] Group 4: Respiratory H₂-evolving [NiFe] hydrogenase
Subgroup	[NiFe] Group 4d: Ferredoxin-coupled, Mrp-linked
Function	Forms respiratory supercomplex that couples oxidation of ferredoxin_red to reduction of protons 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 vents, other high temperature ecosystems
Taxonomic distribution	Exclusive to Thermococci and Aciduliprofundi

Genetic Organisation

e.g. Pyrococcus furiosus (WP_011012581.1):

Architecture

Structures	6CFW (Pyrococcus furiosus, 3.7 Å resolution)
Subunits	14
Subunit description	MbhL (hydrogenase large subunit) MbhJ (hydrogenase small subunit) MbhM (NuoH-like transmembrane adaptor) MbhH (NuoL-like transmembrane adaptor) MchK (NuoC-like transmembrane adaptor) MchABCDEFG (Mrp-like antiporter subunits)
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_014122750.1	Thermococcus sp. AM4	[NiFe] Group 4d	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_011833332.1	Methanocorpusculum labreanum	[NiFe] Group 4d	Euryarchaeota	Methanomicrobiales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_004038443.1	Methanofollis liminatans	[NiFe] Group 4d	Euryarchaeota	Methanomicrobiales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_004077410.1	Methanoplanus limicola	[NiFe] Group 4d	Euryarchaeota	Methanomicrobiales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_013329507.1	Methanoplanus petrolearius	[NiFe] Group 4d	Euryarchaeota	Methanomicrobiales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_011449544.1	Methanospirillum hungatei	[NiFe] Group 4d	Euryarchaeota	Methanomicrobiales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_010867842.1	Pyrococcus abyssi	[NiFe] Group 4d	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_011012581.1	Pyrococcus furiosus	[NiFe] Group 4d	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_010885519.1	Pyrococcus horikoshii	[NiFe] Group 4d	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_013747503.1	Pyrococcus sp. NA2	[NiFe] Group 4d	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_014734412.1	Pyrococcus sp. ST04	[NiFe] Group 4d	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_013905871.1	Pyrococcus yayanosii	[NiFe] Group 4d	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_013467760.1	Thermococcus barophilus	[NiFe] Group 4d	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_012751197.1	Thermococcus gammatolerans	[NiFe] Group 4d	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_011251041.1	Thermococcus kodakarensis	[NiFe] Group 4d	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_004066437.1	Thermococcus litoralis	[NiFe] Group 4d	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_004066458.1	Thermococcus litoralis	[NiFe] Group 4d	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_012572555.1	Thermococcus onnurineus	[NiFe] Group 4d	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_015849571.1	Thermococcus sibiricus	[NiFe] Group 4d	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_014013072.1	Thermococcus sp. 4557	[NiFe] Group 4d	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_014013086.1	Thermococcus sp. 4557	[NiFe] Group 4d	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_010479563.1	Thermococcus zilligii	[NiFe] Group 4d	Euryarchaeota	Thermococcales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_008083483.1	Aciduliprofundum boonei	[NiFe] Group 4d	Euryarchaeota	Unclassified	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_015283654.1	Aciduliprofundum sp. MAR08-339	[NiFe] Group 4d	Euryarchaeota	Unclassified	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_029166411.1	Aminiphilus circumscriptus	[NiFe] Group 4d	Synergistetes	Synergistales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_013048648.1	Aminobacterium colombiense	[NiFe] Group 4d	Synergistetes	Synergistales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_024821984.1	Aminobacterium mobile	[NiFe] Group 4d	Synergistetes	Synergistales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_006301161.1	Aminomonas paucivorans	[NiFe] Group 4d	Synergistetes	Synergistales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_009200527.1	Anaerobaculum hydrogeniformans	[NiFe] Group 4d	Synergistetes	Synergistales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_014807277.1	Anaerobaculum mobile	[NiFe] Group 4d	Synergistetes	Synergistales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_005662523.1	Dethiosulfovibrio peptidovorans	[NiFe] Group 4d	Synergistetes	Synergistales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_009164181.1	Pyramidobacter piscolens	[NiFe] Group 4d	Synergistetes	Synergistales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.
WP_014163350.1	Thermovirga lienii	[NiFe] Group 4d	Synergistetes	Synergistales	Evolving	Sensitive	13	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, two [FeS] proteins, seven MRP antiporter subunits, etc.

Literature

Genetics:

Søndergaard, D., Petersen, C.N.S., and Greening, C. (2017) HydDB: a web tool for hydrogenase classification and analysis. Sci. Rep. 6: 34212.

Physiology:

Kanai, T., Imanaka, H., Nakajima, A., Uwamori, K., Omori, Y., Fukui, T., Atomi, H., and Imanaka, T. (2005) Continuous hydrogen production by the hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1. J. Biotechnol. 116: 271-282.
Kanai, T., Matsuoka, R., Beppu, H., Nakajima, A., Okada, Y., Atomi, H., and Imanaka, T., (2011) Distinct physiological roles of the three [NiFe]-hydrogenase orthologs in the hyperthermophilic archaeon Thermococcus kodakarensis. J. Bacteriol. 193: 3109-3116.
Kanai, T., Simons, J.R., Tsukamoto, R., Nakajima, A., Omori, Y., Matsuoka, R., Beppu, H., Imanaka, T., and Atomi, H. (2015) Overproduction of the membrane-bound [NiFe]-hydrogenase in Thermococcus kodakarensis and its effect on hydrogen production. Front. Microbiol. 6: 847.
Santangelo, T.J. and Reeve, J.N. (2011) Deletion of alternative pathways for reductant recycling in Thermococcus kodakarensis increases hydrogen production. Mol. Microbiol. 81: 897-911.
Sapra, R., Bagramyan, K., and Adams, M.W. (2003) A simple energy-conserving system: proton reduction coupled to proton translocation. Proc. Natl. Acad. Sci. USA 100: 7545-7550.
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.
Schut, G.J., Nixon, W.J., Lipscomb, G.L., Scott, R.A., and Adams, M.W. (2012) Mutational analyses of the enzymes involved in the metabolism of hydrogen by the hyperthermophilic archaeon Pyrococcus furiosus. Front. Microbiol. 3: 163.
Silva, P.J., van den Ban, E.C., Wassink, H., Haaker, H., de Castro, B., Robb, F.T., and Hagen, W.R. (2000) Enzymes of hydrogen metabolism in Pyrococcus furiosus. Eur. J. Biochem. 267: 6541-6551.

Biochemistry:

McTernan, P.M., Chandrayan, S.K., Wu, C.H., Vaccaro, B.J., Lancaster, W.A., and Adams, M.W. (2015) Engineering the respiratory membrane-bound hydrogenase of the hyperthermophilic archaeon Pyrococcus furiosus and characterization of the catalytically active cytoplasmic subcomplex. Prot. Eng. Des. Select. 28: 1-8.
McTernan, P.M., Chandrayan, S.K., Wu, C.H., Vaccaro, B.J., Lancaster, W.A., Yang, Q., Fu, D., Hura, G.L., Tainer, J.A., and Adams, M.W (2014) Intact functional fourteen-subunit respiratory membrane-bound [NiFe]-hydrogenase complex of the hyperthermophilic archaeon Pyrococcus furiosus. J. Biol. Chem. 289: 19364-19372.
Sapra, R., Verhagen, M.F., and Adams, M.W. (2000) Purification and characterization of a membrane-bound hydrogenase from the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 182: 3423-3428.
Yu, H., Wu, C.-H., Schut, G.J., Haja, D.K., Zhao, G., Peters, J.W., Adams, M.W.W., and Li, H. (2018) Structure of an ancient respiratory system. Cell, in press (doi: 10.1016/j.cell.2018.03.071).