[FeFe] Group A3-hydrogenase
This entry was last updated at: Feb. 9, 2018, 6:46 a.m.
Properties
| Group | [FeFe]-hydrogenases |
| Subgroup | [FeFe] Group A3: Bifurcating |
| Function | Bifurcates electrons from H2 to NAD and ferredoxin. Reverse reaction can also occur resulting in reoxidation of redox carriers concomitant with fermentative H2 evolution. |
| Activity | Electron-bifurcation |
| Oxygen tolerance | O2-labile |
| Localisation | Cytosolic |
Distribution
| Ecosystem distribution | Gastrointestinal tracts, anoxic soils and sediments |
| Taxonomic distribution | Widespread in anaerobic bacteria, including Firmicutes, Bacteroidetes, Deltaproteobacteria, and Spirochaetes |
Genetic Organisation
Organisation 1: Thermotoga maritima (WP_004081677.1):
Organisation 2: Desulfovibrio fructosovorans (WP_005990603.1):
Architecture
| Structures |
|
| Subunits | 3 or 4 |
| Subunit description | HydA (catalytic subunit) HydB (diaphorase subunit) HydC (thioredoxin) In organisation 2, an additional thioredoxin (HydD) is present |
| Catalytic site | [FeFe]-centre |
| FeS clusters | Organisation 1: 3 [4Fe4S] clusters, 2 [2Fe2S] clusters Organisation 2: 3 [4Fe4S] clusters, 1 [2Fe2S] cluster |
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_013824004.1 | Desulfotomaculum kuznetsovii | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 2 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_003540305.1 | Desulfotomaculum nigrificans | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 3 | [FeFe]-centre, 2 x [4Fe4S] clusters | NADH dehydrogenase, thioredoxin |
| WP_003541670.1 | Desulfotomaculum nigrificans | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_003543871.1 | Desulfotomaculum nigrificans | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_011876846.1 | Desulfotomaculum reducens | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 3 | [FeFe]-centre, 2 x [4Fe4S] clusters | NADH dehydrogenase, thioredoxin |
| WP_011877994.1 | Desulfotomaculum reducens | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_011877997.1 | Desulfotomaculum reducens | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 2 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_011879575.1 | Desulfotomaculum reducens | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_013840577.1 | Desulfotomaculum ruminis | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_013842391.1 | Desulfotomaculum ruminis | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 2 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_013842395.1 | Desulfotomaculum ruminis | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_013842583.1 | Desulfotomaculum ruminis | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 3 | [FeFe]-centre, 2 x [4Fe4S] clusters | NADH dehydrogenase, thioredoxin |
| WP_013843380.1 | Desulfotomaculum ruminis | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 3 | [FeFe]-centre, 2 x [4Fe4S] clusters | NADH dehydrogenase, thioredoxin |
| WP_027356557.1 | Desulfotomaculum thermocisternum | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_027356646.1 | Desulfotomaculum thermocisternum | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 2 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_027357333.1 | Desulfotomaculum thermocisternum | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_029460330.1 | Desulfovibrio alcoholivorans | [FeFe] Group A3 | Deltaproteobacteria | Desulfovibrionales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 2 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_029460554.1 | Desulfovibrio alcoholivorans | [FeFe] Group A3 | Deltaproteobacteria | Desulfovibrionales | Bifurcating | Labile | 4 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin, thioredoxin |
| WP_005990603.1 | Desulfovibrio fructosivorans | [FeFe] Group A3 | Deltaproteobacteria | Desulfovibrionales | Bifurcating | Labile | 4 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin, thioredoxin |
| WP_005991663.1 | Desulfovibrio fructosivorans | [FeFe] Group A3 | Deltaproteobacteria | Desulfovibrionales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 2 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_024823936.1 | Desulfovibrio magneticus | [FeFe] Group A3 | Deltaproteobacteria | Desulfovibrionales | Bifurcating | Labile | 4 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin, thioredoxin |
| WP_027717485.1 | Desulfovirgula thermocuniculi | [FeFe] Group A3 | Firmicutes | Thermoanaerobacterales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_027718652.1 | Desulfovirgula thermocuniculi | [FeFe] Group A3 | Firmicutes | Thermoanaerobacterales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 2 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_018084282.1 | Desulfurispora thermophila | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_018085930.1 | Desulfurispora thermophila | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 2 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_018086225.1 | Desulfurispora thermophila | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_022847517.1 | Desulfurobacterium sp. TC5-1 | [FeFe] Group A3 | Aquificae | Desulfurobacteriales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_013637757.1 | Desulfurobacterium thermolithotrophum | [FeFe] Group A3 | Aquificae | Desulfurobacteriales | Bifurcating | Labile | 3 | [FeFe]-centre, 2 x [4Fe4S] clusters | NADH dehydrogenase, thioredoxin |
| WP_012548684.1 | Dictyoglomus thermophilum | [FeFe] Group A3 | Dictyoglomi | Dictyoglomales | Bifurcating | Labile | 1 | [FeFe]-centre, 3 x [4Fe4S] clusters, 2 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_012582935.1 | Dictyoglomus turgidum | [FeFe] Group A3 | Dictyoglomi | Dictyoglomales | Bifurcating | Labile | 1 | [FeFe]-centre, 3 x [4Fe4S] clusters, 2 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_005333143.1 | Dorea formicigenerans | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_028086317.1 | Dorea longicatena | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_012414703.1 | Elusimicrobium minutum | [FeFe] Group A3 | Elusimicrobia | Elusimicrobiales | Bifurcating | Labile | 1 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_010753129.1 | Enterococcus asini | [FeFe] Group A3 | Firmicutes | Lactobacillales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_016182069.1 | Enterococcus avium | [FeFe] Group A3 | Firmicutes | Lactobacillales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_010780462.1 | Enterococcus gilvus | [FeFe] Group A3 | Firmicutes | Lactobacillales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_010740236.1 | Enterococcus malodoratus | [FeFe] Group A3 | Firmicutes | Lactobacillales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_010746116.1 | Enterococcus raffinosus | [FeFe] Group A3 | Firmicutes | Lactobacillales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_027088814.1 | Erysipelatoclostridium saccharogumia | [FeFe] Group A3 | Firmicutes | Erysipelotrichales | Bifurcating | Labile | 4 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin, thioredoxin |
| WP_004610503.1 | Erysipelatoclostridium spiroforme | [FeFe] Group A3 | Firmicutes | Erysipelotrichales | Bifurcating | Labile | 4 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin, thioredoxin |
| WP_013486450.1 | Ethanoligenens harbinense | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_013379183.1 | Eubacterium limosum | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_021739954.1 | Eubacterium ramulus | [FeFe] Group A3 | Firmicutes | Clostridiales | Bifurcating | Labile | 4 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin, thioredoxin |
| WP_011993415.1 | Fervidobacterium nodosum | [FeFe] Group A3 | Thermotogae | Thermotogales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 2 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_014451418.1 | Fervidobacterium pennivorans | [FeFe] Group A3 | Thermotogae | Thermotogales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 2 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_015556986.1 | Fretibacterium fastidiosum | [FeFe] Group A3 | Synergistetes | Synergistales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_010680344.1 | Fusobacterium gonidiaformans | [FeFe] Group A3 | Fusobacteria | Fusobacteriales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_005952705.1 | Fusobacterium necrophorum | [FeFe] Group A3 | Fusobacteria | Fusobacteriales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_005980462.1 | Fusobacterium ulcerans | [FeFe] Group A3 | Fusobacteria | Fusobacteriales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
| WP_005950651.1 | Fusobacterium varium | [FeFe] Group A3 | Fusobacteria | Fusobacteriales | Bifurcating | Labile | 3 | [FeFe]-centre, 3 x [4Fe4S] clusters, 1 x [2Fe2S] cluster | NADH dehydrogenase, thioredoxin |
Literature
Genetics:
- Calusinska, M., Happe, T., Joris, B., and Wilmotte, A. (2010) The surprising diversity of clostridial hydrogenases: a comparative genomic perspective. Microbiol. 156: 1575-1588.
- 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.
- Malki, S., Saimmaime, I., De Luca, G., Rousset, M., Dermoun, Z., and Belaich, J.P., (1995) Characterization of an operon encoding an NADP-reducing hydrogenase in Desulfovibrio fructosovorans. J. Bacteriol. 177: 2628-2636.
- Poudel, S., Tokmina-Lukaszewska, M., Colman, D.R., Refai, M., Schut, G.J., King, P.W., Maness, P.C., Adams, M.W., Peters, J.W., Bothner, B., and Boyd, E.S. (2016) Unification of [FeFe]-hydrogenases into three structural and functional groups. BBA Gen. Subj. 1860: 1910-1921.
- Verhagen, M.F., O'Rourke, T. and Adams, M.W. (1999) The hyperthermophilic bacterium, Thermotoga maritima, contains an unusually complex iron-hydrogenase: amino acid sequence analyses versus biochemical characterization. BBA Bioenerg. 1412: 212-229.
- Wolf, P.G., Biswas, A., Morales, S.E., Greening, C., and Gaskins, H.R. (2016) H2 metabolism is widespread and diverse among human colonic microbes. Gut Microb. 7: 235-245.
- Zheng, Y., Kahnt, J., Kwon, I.H., Mackie, R.I., and Thauer, R.K. (2014) Hydrogen formation and its regulation in Ruminococcus albus: involvement of an electron-bifurcating [FeFe]-hydrogenase, of a non-electron-bifurcating [FeFe]-hydrogenase, and of a putative hydrogen-sensing [FeFe]-hydrogenase. J. Bacteriol. 196: 3840-3852.
Physiology:
- Buckel, W. and Thauer, R.K. (2013) Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation. BBA Bioenerg. 1827: 94-113.
- Mock, J., Zheng, Y., Mueller, A.P., Ly, S., Tran, L., Segovia, S., Nagaraju, S., Köpke, M., Dürre, P., and Thauer, R.K. (2015) Energy conservation associated with ethanol formation from H2 and CO2 in Clostridium autoethanogenum involving electron bifurcation. J. Bacteriol. 197: 2965-2980.
- Schuchmann, K. and Müller, V. (2014) Autotrophy at the thermodynamic limit of life: a model for energy conservation in acetogenic bacteria. Nat. Rev. Microbiol. 12: 809-821.
- Wang, S., Huang, H., Kahnt, J., and Thauer, R.K. (2013) A reversible electron-bifurcating ferredoxin-and NAD-dependent [FeFe]-hydrogenase (HydABC) in Moorella thermoacetica. J. Bacteriol. 195: 1267-1275.
Biochemistry:
- Caserta, G., Adamska-Venkatesh, A., Pecqueur, L., Atta, M., Artero, V., Roy, S., Reijerse, E., Lubitz, W., and Fontecave, M. (2016) Chemical assembly of multiple metal cofactors: the heterologously expressed multidomain [FeFe]-hydrogenase from Megasphaera elsdenii. BBA Bioenerg. 1857: 1734-1740.
- Losey, N.A., Mus, F., Peters, J.W., Le, H.M., and McInerney, M.J. (2017) Syntrophomonas wolfei uses an NADH-dependent, ferredoxin-independent [FeFe]-hydrogenase to reoxidize NADH. Appl. Environ. Microbiol. 83: e01335-17.
- Schuchmann, K. and Müller, V. (2012) A bacterial electron-bifurcating hydrogenase. J. Biol. Chem. 287: 31165-31171.
- Schut, G.J. and Adams, M.W. (2009) The iron-hydrogenase of Thermotoga maritima utilizes ferredoxin and NADH synergistically: a new perspective on anaerobic hydrogen production. J. Bacteriol. 191: 4451-4457.
- 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.