[NiFe] Group 3b-hydrogenase

This entry was last updated at: Feb. 9, 2018, 7:34 a.m.

Properties

Group	[NiFe] Group 3: Cofactor-coupled bidirectional [NiFe] hydrogenases
Subgroup	[NiFe] Group 3b: NADP-coupled
Function	Directly couples oxidation of NADPH to fermentative evolution of H₂. Reverse reaction may also occur. Some complexes controversially proposed to harbour sulfhydrogenase activity.
Activity	Bidirectional
Oxygen tolerance	O₂-tolerant
Localisation	Cytosolic

Distribution

Ecosystem distribution	Diverse soil and aquatic environments
Taxonomic distribution	Encoded in multiple diverse bacterial and archaeal phyla

Genetic Organisation

e.g. Pyrococcus furiosus (WP_011012029.1):

Architecture

Structures	5ODC (Methanothermococcus thermolithotrophicus, 2.3 Å resolution) 5ODH (Methanothermococcus thermolithotrophicus, 2.2 Å resolution, bound with heterodisulfide) 5ODI (Methanothermococcus thermolithotrophicus, 2.4 Å resolution, bound with coenzyme M)
Subunits	4
Subunit description	HyhL (hydrogenase large subunit) HyhS (hydrogenase small subunit) HyhG (diaphorase catalytic subunit) HyhB (diaphorase electron transfer subunit)
Catalytic site	[NiFe]-centre
FeS clusters	Proximal: 4Cys[4Fe4S] Medial: 4Cys[4Fe4S] Distal: 4Cys[4Fe4S]

Important Notes

Despite the ubiquitous nature of this hydrogenase, the enzyme has only been purified from Pyrococcus furiosus. It remains unclear whether bacterial enzymes are also NADP⁺-specific.

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_013749130.1	Pyrococcus sp. NA2	[NiFe] Group 3b	Euryarchaeota	Thermococcales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_013904776.1	Pyrococcus yayanosii	[NiFe] Group 3b	Euryarchaeota	Thermococcales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_013905579.1	Pyrococcus yayanosii	[NiFe] Group 3b	Euryarchaeota	Thermococcales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_013923702.1	Francisella sp. TX077308	[NiFe] Group 3b	Gammaproteobacteria	Thiotrichales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_013979629.1	Eggerthella sp. YY7918	[NiFe] Group 3b	Actinobacteria	Coriobacteriales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_014012081.1	Thermococcus sp. 4557	[NiFe] Group 3b	Euryarchaeota	Thermococcales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_014012582.1	Thermococcus sp. 4557	[NiFe] Group 3b	Euryarchaeota	Thermococcales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_014029204.1	Acidithiobacillus ferrivorans	[NiFe] Group 3b	Gammaproteobacteria	Acidithiobacillales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_014068049.1	Rhodothermus marinus	[NiFe] Group 3b	Bacteroidetes	Unclassified	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_014122569.1	Thermococcus sp. AM4	[NiFe] Group 3b	Euryarchaeota	Thermococcales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_014292817.1	Oceanimonas sp. GK1	[NiFe] Group 3b	Gammaproteobacteria	Aeromonadales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_014433201.1	Caldilinea aerophila	[NiFe] Group 3b	Chloroflexi	Caldilineales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_014558156.1	Fervidicoccus fontis	[NiFe] Group 3b	Crenarchaeota	Fervidicoccales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_014677317.1	Streptomyces hygroscopicus	[NiFe] Group 3b	Actinobacteria	Actinomycetales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_014734005.1	Pyrococcus sp. ST04	[NiFe] Group 3b	Euryarchaeota	Thermococcales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_014734228.1	Pyrococcus sp. ST04	[NiFe] Group 3b	Euryarchaeota	Thermococcales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_014737726.1	Thermogladius cellulolyticus	[NiFe] Group 3b	Crenarchaeota	Desulfurococcales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_014788000.1	Thermococcus sp. CL1	[NiFe] Group 3b	Euryarchaeota	Thermococcales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_014788486.1	Thermococcus sp. CL1	[NiFe] Group 3b	Euryarchaeota	Thermococcales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_014814971.1	Mycobacterium chubuense	[NiFe] Group 3b	Actinobacteria	Actinomycetales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_014890330.1	Methylocystis sp. SC2	[NiFe] Group 3b	Alphaproteobacteria	Rhizobiales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_015051716.1	Thermacetogenium phaeum	[NiFe] Group 3b	Firmicutes	Thermoanaerobacterales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_015258948.1	Thioalkalivibrio nitratireducens	[NiFe] Group 3b	Gammaproteobacteria	Chromatiales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_015283468.1	Aciduliprofundum sp. MAR08-339	[NiFe] Group 3b	Euryarchaeota	Unclassified	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_015403594.1	Desulfocapsa sulfexigens	[NiFe] Group 3b	Deltaproteobacteria	Desulfobacterales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_015662841.1	Streptomyces davawensis	[NiFe] Group 3b	Actinobacteria	Actinomycetales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_015720565.1	Geobacter sp. M18	[NiFe] Group 3b	Deltaproteobacteria	Desulfuromonadales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_015760489.1	Eggerthella lenta	[NiFe] Group 3b	Actinobacteria	Coriobacteriales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_015790329.1	Halorhabdus utahensis	[NiFe] Group 3b	Euryarchaeota	Halobacteriales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_015837532.1	Geobacter sp. M21	[NiFe] Group 3b	Deltaproteobacteria	Desulfuromonadales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_015848571.1	Thermococcus sibiricus	[NiFe] Group 3b	Euryarchaeota	Thermococcales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_015849791.1	Thermococcus sibiricus	[NiFe] Group 3b	Euryarchaeota	Thermococcales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_016308610.1	Enterorhabdus caecimuris	[NiFe] Group 3b	Actinobacteria	Coriobacteriales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_016920195.1	Methylocystis parvus	[NiFe] Group 3b	Alphaproteobacteria	Rhizobiales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_017290644.1	Leptolyngbya boryana	[NiFe] Group 3b	Cyanobacteria	Oscillatoriales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_017774733.1	Burkholderia kururiensis	[NiFe] Group 3b	Betaproteobacteria	Burkholderiales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_017873497.1	Caldatribacterium saccharofermentans	[NiFe] Group 3b	Atribacteria	Unclassified	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_017890430.1	Caldatribacterium californiense	[NiFe] Group 3b	Atribacteria	Unclassified	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_018160400.1	Smaragdicoccus niigatensis	[NiFe] Group 3b	Actinobacteria	Actinomycetales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_018265836.1	Methylosinus sp. LW4	[NiFe] Group 3b	Alphaproteobacteria	Rhizobiales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_018290138.1	Verrucomicrobium sp. 3C	[NiFe] Group 3b	Verrucomicrobia	Verrucomicrobiales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_018300187.1	Fangia hongkongensis	[NiFe] Group 3b	Gammaproteobacteria	Thiotrichales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_018384886.1	Streptomyces vitaminophilus	[NiFe] Group 3b	Actinobacteria	Actinomycetales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_018407885.1	Methylocystis rosea	[NiFe] Group 3b	Alphaproteobacteria	Rhizobiales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_018508430.1	Thiobacillus thioparus	[NiFe] Group 3b	Betaproteobacteria	Hydrogenophilales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_018608874.1	Uliginosibacterium gangwonense	[NiFe] Group 3b	Betaproteobacteria	Rhodocyclales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_019350089.1	Fluoribacter dumoffii	[NiFe] Group 3b	Gammaproteobacteria	Legionellales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_020123404.1	Streptomyces canus	[NiFe] Group 3b	Actinobacteria	Actinomycetales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_020412786.1	Microbulbifer variabilis	[NiFe] Group 3b	Gammaproteobacteria	Alteromonadales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein
WP_020524726.1	Catelliglobosispora koreensis	[NiFe] Group 3b	Actinobacteria	Actinomycetales	Bidirectional	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Diaphorase, [FeS] protein

Literature

Genetics:

Berney, M., Greening, C., Hards, K., Collins, D., and Cook, G.M. (2014) Three different [NiFe] hydrogenases confer metabolic flexibility in the obligate aerobe Mycobacterium smegmatis. Environ. Microbiol. 16: 318-330.
Chandrayan, S.K., McTernan, P.M., Hopkins, R.C., Sun, J., Jenney, F.E., and Adams, M.W. (2012) Engineering hyperthermophilic archaeon Pyrococcus furiosus to overproduce its cytoplasmic [NiFe]-hydrogenase. J. Biol. Chem. 287: 3257-3264.
Greening, C., Biswas, A., Carere, C.R., Jackson, C.J., Taylor, M.C., Stott, M.B., Cook, G.M., and Morales, S.E. (2016) Genomic and metagenomic surveys of hydrogenase distribution indicate H₂ is a widely utilised energy source for microbial growth and survival. ISME J. 10: 761-777.
Mohapatra, A., Leul, M., Sandström, G., and Sellstedt, A. (2006) Occurrence and characterisation of the hydrogen-evolving enzyme in Frankia sp. Int. J. Hydrogen Energy 31: 1445-1451.
Sun, J., Hopkins, R.C., Jenney Jr, F.E., McTernan, P.M., and Adams, M.W. (2010) Heterologous expression and maturation of an NADP-dependent [NiFe]-hydrogenase: a key enzyme in biofuel production. PLOS One 5: e10526.
Vignais, P.M., Billoud, B., and Meyer, J. (2001) Classification and phylogeny of hydrogenases. FEMS Microbiol. Rev. 25: 455-501.

Physiology:

Arendsen, A.F., Veenhuizen, P.T.M., and Hagen, W.R. (1995) Redox properties of the sulfhydrogenase from Pyrococcus furiosus. FEBS Lett. 368: 117-121.
Berney, M., Greening, C., Conrad, R., Jacobs, W.R., and Cook, G.M. (2014) An obligately aerobic soil bacterium activates fermentative hydrogen production to survive reductive stress during hypoxia. Proc. Natl. Acad. Sci. U. S. A. 111: 11479-11484.
Carere, C.R., Hards, K., Houghton, K.M., Power, J.F., McDonald, B., Collet, C., Gapes, D.J., Sparling, R., Boyd, E.S., Cook, G.M., Greening, C., and Stott, M.B. (2017) Mixotrophy drives niche expansion of verrucomicrobial methanotrophs. ISME J. 11: 2599-2610.
Pedroni, P., Della Volpe, A., Galli, G., Mura, G.M., Pratesi, C., and Grandi, G. (1995) Characterization of the locus encoding the [Ni-Fe] sulfhydrogenase from the archaeon Pyrococcus furiosus: evidence for a relationship to bacterial sulfite reductases. Microbiol. 141: 449-458.
Yoon, K.S., Ueda, Y., Ishii, M., Igarashi, Y., and Kodama, T. (1996) NADH: ferredoxin reductase and NAD-reducing hydrogenase activities in Hydrogenobacter thermophilus strain TK-6. FEMS Microbiol. Lett. 139: 139-142.

Biochemistry:

Bryant, F.O. and Adams, M.W. (1989) Characterization of hydrogenase from the hyperthermophilic archaebacterium, Pyrococcus furiosus. J. Biol. Chem. 264: 5070-5079.
Greene, B.L., Vansuch, G.E., Wu, C.H., Adams, M.W., and Dyer, R.B. (2016) Glutamate gated proton-coupled electron transfer activity of a [NiFe]-hydrogenase. J. Am. Chem. Soc. 138: 13013-13021.
Kanai, T., Ito, S., and Imanaka, T. (2003) Characterization of a cytosolic NiFe-hydrogenase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J. Bacteriol. 185: 1705-1711.
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.
Kwan, P., McIntosh, C.L., Jennings, D.P., Hopkins, R.C., Chandrayan, S.K., Wu, C.H., Adams, M.W., and Jones, A.K. (2015) The [NiFe]-hydrogenase of Pyrococcus furiosus exhibits a new type of oxygen tolerance. J. Am. Chem. Soc. 137: 13556-13565.
Ma, K. and Adams, M.W. (2000) Hydrogenases I and II from Pyrococcus furiosus. Meth. Enzymol. 331: 208-216.
Ma, K., Schicho, R.N., Kelly, R.M., and Adams, M.W. (1993) Hydrogenase of the hyperthermophile Pyrococcus furiosus is an elemental sulfur reductase or sulfhydrogenase: evidence for a sulfur-reducing hydrogenase ancestor. Proc. Natl. Acad. Sci. USA 90: 5341-5344.
Ma, K., Weiss, R. and Adams, M.W. (2000) Characterization of hydrogenase II from the hyperthermophilic archaeon Pyrococcus furiosus and assessment of its role in sulfur reduction. J. Bacteriol. 182: 1864-1871.
Ma, K., Zhou, H.Z. and Adams, M.W. (1994) Hydrogen production from pyruvate by enzymes purified from the hyperthermophilic archaeon, Pyrococcus furiosus: a key role for NADPH. FEMS Microbiol. Lett. 122: 245-250.
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. Engin. Des. Select. 28: 1-8.
Mohapatra, A., Leul, M., Mattsson, U., and Sellstedt, A. (2004) A hydrogen-evolving enzyme is present in Frankia sp. R43. FEMS Microbiol. Lett. 236: 235-240.
Rákhely, G., Zhou, Z.H., Adams, M.W., and Kovács, K.L. (1999) Biochemical and molecular characterization of the [NiFe] hydrogenase from the hyperthermophilic archaeon, Thermococcus litoralis. Eur. J. Biochem. 266: 1158-1165.
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., de Castro, B., and Hagen, W.R. (1999) On the prosthetic groups of the NiFe sulfhydrogenase from Pyrococcus furiosus: topology, structure, and temperature-dependent redox chemistry. J. Biol. Inorg. Chem. 4: 284-291.
Thorgersen, M.P., Stirrett, K., Scott, R.A., and Adams, M.W. (2012) Mechanism of oxygen detoxification by the surprisingly oxygen-tolerant hyperthermophilic archaeon, Pyrococcus furiosus. Proc. Natl. Acad. Sci. USA 109: 18547-18552.
Wagner, T., Koch, J., Ermler, U., and Shima, S. (2017) Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction. Science 357: 699-703.

Chemistry:

Greene, B.L., Wu, C.H., McTernan, P.M., Adams, M.W. and Dyer, R.B. (2015) Proton-coupled electron transfer dynamics in the catalytic mechanism of a [NiFe]-hydrogenase. J. Am. Chem. Soc. 137: 4558-4566.