[NiFe] Group 4e-hydrogenase

This entry was last updated at: June 13, 2016, 11:11 a.m.

Properties

Group	[NiFe] Group 4: Respiratory H₂-evolving [NiFe] hydrogenases
Subgroup	[NiFe] Group 4e: Ferredoxin-coupled, Ech-type
Function	Forms respiratory complex that couples oxidation of ferredoxin_red to reduction of protons to H₂ in acetoclastic methanogenesis. This process appears to be coupled to sodium or proton translocation through the transmembrane modules. The complex can also act in the reverse direction during hydrogenotrophic methanogenesis.
Activity	Bidirectional
Oxygen tolerance	O₂-sensitive
Localisation	Membrane-bound

Distribution

Ecosystem distribution	Anoxic soils and sediments, animal gastrointestinal tracts
Taxonomic distribution	Encoded in multiple methanogenic orders and anaerobic bacteria

Genetic Organisation

e.g. Methanosarcina barkeri (WP_011305188.1):

Architecture

Structures	None
Subunits	6
Subunit description	EchA (hydrogenase large subunit) EchC (hydrogenase small subunit) EchF (iron-sulfur subunit) EchB (NuoH-like transmembrane adaptor) EchA (NuoL-like transmembrane adaptor) EchD (NuoC-like transmembrane adaptor)
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_012798463.1	Slackia heliotrinireducens	[NiFe] Group 4e	Actinobacteria	Coriobacteriales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_009138996.1	Slackia piriformis	[NiFe] Group 4e	Actinobacteria	Coriobacteriales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_009078628.1	Slackia sp. CM382	[NiFe] Group 4e	Actinobacteria	Coriobacteriales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_010936594.1	Dehalococcoides mccartyi	[NiFe] Group 4e	Chloroflexi	Dehalococcoidales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_013537236.1	Thermovibrio ammonificans	[NiFe] Group 4e	Aquificae	Desulfobacterales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_020585229.1	Desulfobacter curvatus	[NiFe] Group 4e	Deltaproteobacteria	Desulfobacterales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_021758533.1	Desulfovibrio gigas	[NiFe] Group 4e	Deltaproteobacteria	Desulfobacterales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_028587759.1	Desulfocurvus vexinensis	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_028576381.1	Desulfomicrobium escambiense	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_028573897.1	Desulfonatronovibrio hydrogenovorans	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_028572004.1	Desulfonatronum lacustre	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_029967123.1	Desulfonauticus sp. A7A	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_013515288.1	Desulfovibrio aespoeensis	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_005986921.1	Desulfovibrio africanus	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_020887613.1	Desulfovibrio alkalitolerans	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_027178908.1	Desulfovibrio bastinii	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_027187946.1	Desulfovibrio cuneatus	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_012625292.1	Desulfovibrio desulfuricans	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_014323623.1	Desulfovibrio desulfuricans	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_015336113.1	Desulfovibrio hydrothermalis	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_027182881.1	Desulfovibrio inopinatus	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_022661459.1	Desulfovibrio longus	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_012749853.1	Desulfovibrio magneticus	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_018125731.1	Desulfovibrio oxyclinae	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_015414775.1	Desulfovibrio piezophilus	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_027190463.1	Desulfovibrio putealis	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_015853104.1	Desulfovibrio salexigens	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_007524167.1	Desulfovibrio sp. A2	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_020879492.1	Desulfovibrio sp. X2	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_010937737.1	Desulfovibrio vulgaris	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_027723401.1	Desulfovibrio zosterae	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_013638341.1	Desulfurobacterium thermolithotrophum	[NiFe] Group 4e	Aquificae	Desulfurobacteriales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_027716617.1	Desulfuromonas sp. TF	[NiFe] Group 4e	Deltaproteobacteria	Desulfuromonadales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_015720170.1	Geobacter sp. M18	[NiFe] Group 4e	Deltaproteobacteria	Desulfuromonadales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_011937735.1	Geobacter uraniireducens	[NiFe] Group 4e	Deltaproteobacteria	Desulfuromonadales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_015536221.1	Eubacterium cylindroides	[NiFe] Group 4e	Firmicutes	Erysipelotrichales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_022790212.1	Streptococcus pleomorphus	[NiFe] Group 4e	Firmicutes	Lactobacilliales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_012035507.1	Methanocella arvoryzae	[NiFe] Group 4e	Euryarchaeota	Methanocellales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_014405402.1	Methanocella conradii	[NiFe] Group 4e	Euryarchaeota	Methanocellales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_012899275.1	Methanocella paludicola	[NiFe] Group 4e	Euryarchaeota	Methanocellales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_012899230.1	Methanocella paludicola	[NiFe] Group 4e	Euryarchaeota	Methanocellales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_014867437.1	Methanoculleus bourgensis	[NiFe] Group 4e	Euryarchaeota	Methanomicrobiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_011843203.1	Methanoculleus marisnigri	[NiFe] Group 4e	Euryarchaeota	Methanomicrobiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_004039320.1	Methanofollis liminatans	[NiFe] Group 4e	Euryarchaeota	Methanomicrobiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_020449518.1	Methanomassiliicoccus intestinalis	[NiFe] Group 4e	Euryarchaeota	Methanomicrobiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_019176382.1	Methanomassiliicoccus luminyensis	[NiFe] Group 4e	Euryarchaeota	Methanomicrobiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_004077817.1	Methanoplanus limicola	[NiFe] Group 4e	Euryarchaeota	Methanomicrobiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_013328417.1	Methanoplanus petrolearius	[NiFe] Group 4e	Euryarchaeota	Methanomicrobiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_011991040.1	Methanoregula boonei	[NiFe] Group 4e	Euryarchaeota	Methanomicrobiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_015284201.1	Methanoregula formicica	[NiFe] Group 4e	Euryarchaeota	Methanomicrobiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein

Literature

Genetics:

Biswas, R., Zheng, T., Olson, D.G., Lynd, L.R., and Guss, A.M. (2015) Elimination of hydrogenase active site assembly blocks H₂ production and increases ethanol yield in Clostridium thermocellum. Biotechnol. Biofuels 8: 20.
Calusinska, M., Happe, T., Joris, B., and Wilmotte, A. (2010) The surprising diversity of clostridial hydrogenases: a comparative genomic perspective. Microbiol. 156: 1575-1588.
Friedrich, T. and Scheide, D. (2000) The respiratory complex I of bacteria, archaea and eukarya and its module common with membrane-bound multisubunit hydrogenases. FEBS Lett. 479: 1-5.
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.
Hedderich, R. (2004) Energy-converting [NiFe] hydrogenases from archaea and extremophiles: ancestors of complex I. J. Bioenerg. Biomembranes 36: 65-75.
Marreiros, B.C., Batista, A.P., Duarte, A.M., and Pereira, M.M. (2013) A missing link between complex I and group 4 membrane-bound [NiFe] hydrogenases. BBA Bioenerg. 1827: 198-209.
Plugge, C.M., Scholten, J.C., Culley, D.E., Nie, L., Brockman, F.J., and Zhang, W. (2010) Global transcriptomics analysis of the Desulfovibrio vulgaris change from syntrophic growth with Methanosarcina barkeri to sulfidogenic metabolism. Microbiol. 156: 2746-2756.
Rodrigues, R., Valente, F.M., Pereira, I.A., Oliveira, S., and Rodrigues-Pousada, C. (2003) A novel membrane-bound Ech [NiFe] hydrogenase in Desulfovibrio gigas. Biochem. Biophys. Res. Commun. 306: 366-375.

Physiology:

Guss, A.M., Mukhopadhyay, B., Zhang, J.K., and Metcalf, W.W. (2005) Genetic analysis of mch mutants in two Methanosarcina species demonstrates multiple roles for the methanopterin-dependent C-1 oxidation/reduction pathway and differences in H₂ metabolism between closely related species. Mol. Microbiol. 55: 1671-1680.
Hedderich, R. and Forzi, L. (2006) Energy-converting [NiFe] hydrogenases: more than just H₂ activation. J. Mol. Microbiol. Biotechnol. 10: 92-104.
Künkel, A., Vorholt, J.A., Thauer, R.K., and Hedderich, R. (1998) An Escherichia coli hydrogenase-3-type hydrogenase in methanogenic archaea. Eur. J. Biochem. 252: 467-476.
Meuer, J., Kuettner, H.C., Zhang, J.K., Hedderich, R., and Metcalf, W.W. (2002) Genetic analysis of the archaeon Methanosarcina barkeri Fusaro reveals a central role for Ech hydrogenase and ferredoxin in methanogenesis and carbon fixation. Proc. Natl. Acad. Sci. USA 99: 5632-5637.
Morais-Silva, F.O., Santos, C.I., Rodrigues, R., Pereira, I.A., and Rodrigues-Pousada, C. (2013) Roles of HynAB and Ech, the only two hydrogenases found in the model sulfate reducer Desulfovibrio gigas. J. Bacteriol. 195: 4753-4760.
Thauer, R.K., 2012. The Wolfe cycle comes full circle. Proc. Acad. Natl. Sci. USA 109: 15084-15085.
Thauer, R.K., Kaster, A.K., Seedorf, H., Buckel, W., and Hedderich, R. (2008) Methanogenic archaea: ecologically relevant differences in energy conservation. Nat. Rev. Microbiol. 6: 579-591.
Welte, C., Krätzer, C., and Deppenmeier, U. (2010) Involvement of Ech hydrogenase in energy conservation of Methanosarcina mazei. FEBS J. 277:

Biochemistry:

Forzi, L., Koch, J., Guss, A.M., Radosevich, C.G., Metcalf, W.W., and Hedderich, R. (2005) Assignment of the [4Fe-4S] clusters of Ech hydrogenase from Methanosarcina barkeri to individual subunits via the characterization of site-directed mutants. FEBS J. 272: 4741-4753.
Kurkin, S., Meuer, J., Koch, J., Hedderich, R., and Albracht, S.P. (2002) The membrane-bound [NiFe]-hydrogenase (Ech) from Methanosarcina barkeri: unusual properties of the iron-sulphur clusters. Eur. J. Biochem. 269: 6101-6111.
Meuer, J., Bartoschek, S., Koch, J., Künkel, A. and Hedderich, R. (1999) Purification and catalytic properties of Ech hydrogenase from Methanosarcina barkeri. Eur. J. Biochem. 265: 325-335.
Soboh, B., Linder, D., and Hedderich, R. (2004) A multisubunit membrane-bound [NiFe] hydrogenase and an NADH-dependent Fe-only hydrogenase in the fermenting bacterium Thermoanaerobacter tengcongensis. Microbiol. 150: 2451-2463.