[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_013460916.1	Sulfuricurvum kujiense	[NiFe] Group 4e	Epsilonproteobacteria	Campylobacterales	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_008340210.1	Sulfurimonas gotlandica	[NiFe] Group 4e	Epsilonproteobacteria	Campylobacterales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_012969568.1	Allochromatium vinosum	[NiFe] Group 4e	Gammaproteobacteria	Chromatiales	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_015282154.1	Thioflavicoccus mobilis	[NiFe] Group 4e	Gammaproteobacteria	Chromatiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_010251151.1	Acetivibrio cellulolyticus	[NiFe] Group 4e	Firmicutes	Clostridiales	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_027399701.1	Anaerovorax odorimutans	[NiFe] Group 4e	Firmicutes	Clostridiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_027203889.1	Butyrivibrio fibrisolvens	[NiFe] Group 4e	Firmicutes	Clostridiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_026651247.1	Butyrivibrio proteoclasticus	[NiFe] Group 4e	Firmicutes	Clostridiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_026892028.1	Clostridium aerotolerans	[NiFe] Group 4e	Firmicutes	Clostridiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_005213155.1	Clostridium celatum	[NiFe] Group 4e	Firmicutes	Clostridiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_027631079.1	Clostridium cellobioparum	[NiFe] Group 4e	Firmicutes	Clostridiales	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_014254276.1	Clostridium clariflavum	[NiFe] Group 4e	Firmicutes	Clostridiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_024832561.1	Clostridium josui	[NiFe] Group 4e	Firmicutes	Clostridiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_024346172.1	Clostridium methoxybenzovorans	[NiFe] Group 4e	Firmicutes	Clostridiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_004618281.1	Clostridium papyrosolvens	[NiFe] Group 4e	Firmicutes	Clostridiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_004628623.1	Clostridium termitidis	[NiFe] Group 4e	Firmicutes	Clostridiales	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_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_012302199.1	Desulforudis audaxviator	[NiFe] Group 4e	Firmicutes	Clostridiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_027871860.1	Eubacterium cellulosolvens	[NiFe] Group 4e	Firmicutes	Clostridiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_026835345.1	Eubacterium xylanophilum	[NiFe] Group 4e	Firmicutes	Clostridiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_012199760.1	Lachnoclostridium phytofermentans	[NiFe] Group 4e	Firmicutes	Clostridiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_027431522.1	Lachnospira multipara	[NiFe] Group 4e	Firmicutes	Clostridiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_028241974.1	Pseudobutyrivibrio ruminis	[NiFe] Group 4e	Firmicutes	Clostridiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_028246016.1	Pseudobutyrivibrio ruminis	[NiFe] Group 4e	Firmicutes	Clostridiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_028234750.1	Pseudobutyrivibrio sp. MD2005	[NiFe] Group 4e	Firmicutes	Clostridiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_003514863.1	Ruminiclostridium thermocellum	[NiFe] Group 4e	Firmicutes	Clostridiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_007047619.1	Subdoligranulum variabile	[NiFe] Group 4e	Firmicutes	Clostridiales	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_013174844.1	Syntrophothermus lipocalidus	[NiFe] Group 4e	Firmicutes	Clostridiales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_022739883.1	Adlercreutzia equolifaciens	[NiFe] Group 4e	Actinobacteria	Coriobacteriales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_006235754.1	Collinsella aerofaciens	[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_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_006720658.1	Collinsella stercoris	[NiFe] Group 4e	Actinobacteria	Coriobacteriales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_009142078.1	Collinsella tanakaei	[NiFe] Group 4e	Actinobacteria	Coriobacteriales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_012803120.1	Cryptobacterium curtum	[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
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_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_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_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_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_016308760.1	Enterorhabdus caecimuris	[NiFe] Group 4e	Actinobacteria	Coriobacteriales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_028026344.1	Enterorhabdus mucosicola	[NiFe] Group 4e	Actinobacteria	Coriobacteriales	Evolving	Sensitive	6	[NiFe]-centre, 1 x [4Fe4S] clusters	NuoL, NuoH, NuoC, [FeS] protein
WP_006361427.1	Slackia exigua	[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.