[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_013328417.1	Methanoplanus petrolearius	[NiFe] Group 4e	Euryarchaeota	Methanomicrobiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_013403527.1	Caldicellulosiruptor hydrothermalis	[NiFe] Group 4e	Firmicutes	Thermoanaerobacterales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_013411862.1	Caldicellulosiruptor owensensis	[NiFe] Group 4e	Firmicutes	Thermoanaerobacterales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_013432390.1	Caldicellulosiruptor kristjanssonii	[NiFe] Group 4e	Firmicutes	Thermoanaerobacterales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_013460916.1	Sulfuricurvum kujiense	[NiFe] Group 4e	Epsilonproteobacteria	Campylobacterales	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_013537236.1	Thermovibrio ammonificans	[NiFe] Group 4e	Aquificae	Desulfobacterales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_013625216.1	Syntrophobotulus glycolicus	[NiFe] Group 4e	Firmicutes	Clostridiales	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_013786935.1	Thermoanaerobacterium xylanolyticum	[NiFe] Group 4e	Firmicutes	Thermoanaerobacterales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_013979777.1	Eggerthella sp. YY7918	[NiFe] Group 4e	Actinobacteria	Coriobacteriales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_014042067.1	Caldicellulosiruptor lactoaceticus	[NiFe] Group 4e	Firmicutes	Thermoanaerobacterales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_014062054.1	Thermoanaerobacter wiegelii	[NiFe] Group 4e	Firmicutes	Thermoanaerobacterales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_014254276.1	Clostridium clariflavum	[NiFe] Group 4e	Firmicutes	Clostridiales	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_014405402.1	Methanocella conradii	[NiFe] Group 4e	Euryarchaeota	Methanocellales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_014757614.1	Thermoanaerobacterium saccharolyticum	[NiFe] Group 4e	Firmicutes	Thermoanaerobacterales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_014777057.1	Thiocystis violascens	[NiFe] Group 4e	Gammaproteobacteria	Chromatiales	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_015051201.1	Thermacetogenium phaeum	[NiFe] Group 4e	Firmicutes	Thermoanaerobacterales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_015282154.1	Thioflavicoccus mobilis	[NiFe] Group 4e	Gammaproteobacteria	Chromatiales	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
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_015414775.1	Desulfovibrio piezophilus	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	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_015654365.1	Sulfuricurvum sp. RIFRC-1	[NiFe] Group 4e	Epsilonproteobacteria	Campylobacterales	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_015738579.1	Ammonifex degensii	[NiFe] Group 4e	Firmicutes	Clostridiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_015760641.1	Eggerthella lenta	[NiFe] Group 4e	Actinobacteria	Coriobacteriales	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_015926708.1	Clostridium cellulolyticum	[NiFe] Group 4e	Firmicutes	Clostridiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_016308760.1	Enterorhabdus caecimuris	[NiFe] Group 4e	Actinobacteria	Coriobacteriales	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_018962513.1	Coprothermobacter platensis	[NiFe] Group 4e	Firmicutes	Thermoanaerobacterales	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_019226287.1	Dehalobacter sp. E1	[NiFe] Group 4e	Firmicutes	Clostridiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_019907186.1	Thermoanaerobacter indiensis	[NiFe] Group 4e	Firmicutes	Thermoanaerobacterales	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_020490799.1	Dehalobacter sp. FTH1	[NiFe] Group 4e	Firmicutes	Clostridiales	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_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_020887613.1	Desulfovibrio alkalitolerans	[NiFe] Group 4e	Deltaproteobacteria	Desulfovibrionales	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_021900040.1	Eggerthella sp. CAG:1427	[NiFe] Group 4e	Actinobacteria	Coriobacteriales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_022094158.1	Collinsella sp. CAG:166	[NiFe] Group 4e	Actinobacteria	Coriobacteriales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_022106764.1	Dialister sp. CAG:486	[NiFe] Group 4e	Firmicutes	Selenomonadales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_022184688.1	Eggerthella sp. CAG:209	[NiFe] Group 4e	Actinobacteria	Coriobacteriales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_022349360.1	Collinsella sp. CAG:398	[NiFe] Group 4e	Actinobacteria	Coriobacteriales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_022363091.1	Eggerthella sp. CAG:298	[NiFe] Group 4e	Actinobacteria	Coriobacteriales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_022379545.1	Cryptobacterium sp. CAG:338	[NiFe] Group 4e	Actinobacteria	Coriobacteriales	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.