[NiFe] Group 1f-hydrogenase
This entry was last updated at: Feb. 9, 2018, 7:32 a.m.
Properties
| Group | [NiFe] Group 1: Respiratory H2-uptake [NiFe] hydrogenases |
| Subgroup | [NiFe] Group 1f: Oxygen-protecting |
| Function | Unresolved role. Some enzymes mediate hydrogenotrophic respiration using O2 as a terminal electron acceptor. Enzyme also linked to protection from reactive oxygen species, protection of nitrogenase protection, and recycling of nitrogenase-derived H2. |
| Activity | H2-uptake (unidirectional)? |
| Oxygen tolerance | O2-tolerant? |
| Localisation | Membrane-bound |
Distribution
| Ecosystem distribution | Various soil and aquatic environments |
| Taxonomic distribution | Present in both aerobic soil bacteria (e.g. Actinobacteria) and anaerobic marine bacteria (e.g. Deltaproteobacteria) |
Genetic Organisation
e.g. Geobacter sulfurreducens (WP_010940798.1):
Architecture
| Structures |
|
| Subunits | 3 |
| Subunit description | HyoL (hydrogenase large subunit) HyoS (hydrogenase small subunit) HyoE (cytochrome b subunit) |
| Catalytic site | [NiFe]-centre |
| FeS clusters | Proximal: 3Cys1Asp[4Fe4S] or 3Cys1Asn[4Fe4S] Medial: 3Cys[3Fe4S] Distal: 3Cys1His[4Fe4S] |
Important Notes
This hydrogenase class has been minimally studied. Further genetic, physiological, and biochemical studies are required to understand its role and behaviour. There is some phylogenetic evidence that this class is polyphyletic and may in fact include several loosely-related hydrogenases with distinct roles.
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_012421152.1 | Akkermansia muciniphila | [NiFe] Group 1f | Verrucomicrobia | Verrucomicrobiales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_022397361.1 | Akkermansia sp. CAG:344 | [NiFe] Group 1f | Verrucomicrobia | Verrucomicrobiales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_028842875.1 | Thermodesulfovibrio islandicus | [NiFe] Group 1f | Nitrospirae | Nitrospirales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_028845527.1 | Thermodesulfovibrio thiophilus | [NiFe] Group 1f | Nitrospirae | Nitrospirales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_012546172.1 | Thermodesulfovibrio yellowstonii | [NiFe] Group 1f | Nitrospirae | Nitrospirales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_020489980.1 | Dehalobacter sp. FTH1 | [NiFe] Group 1f | Firmicutes | Clostridiales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_027713781.1 | Desulfuromonas sp. TF | [NiFe] Group 1f | Deltaproteobacteria | Desulfuromonadales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_012529798.1 | Geobacter bemidjiensis | [NiFe] Group 1f | Deltaproteobacteria | Desulfuromonadales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_026840074.1 | Geobacter bremensis | [NiFe] Group 1f | Deltaproteobacteria | Desulfuromonadales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_012470110.1 | Geobacter lovleyi | [NiFe] Group 1f | Deltaproteobacteria | Desulfuromonadales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_004512555.1 | Geobacter metallireducens | [NiFe] Group 1f | Deltaproteobacteria | Desulfuromonadales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_015718812.1 | Geobacter sp. M18 | [NiFe] Group 1f | Deltaproteobacteria | Desulfuromonadales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_010940798.1 | Geobacter sulfurreducens | [NiFe] Group 1f | Deltaproteobacteria | Desulfuromonadales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_011937483.1 | Geobacter uraniireducens | [NiFe] Group 1f | Deltaproteobacteria | Desulfuromonadales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_020678214.1 | Geopsychrobacter electrodiphilus | [NiFe] Group 1f | Deltaproteobacteria | Desulfuromonadales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_025324524.1 | Deferrisoma camini | [NiFe] Group 1f | Deltaproteobacteria | Unclassified | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_013450229.1 | Calditerrivibrio nitroreducens | [NiFe] Group 1f | Deferribacteres | Deferribacterales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_013006836.1 | Deferribacter desulfuricans | [NiFe] Group 1f | Deferribacteres | Deferribacterales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_013011747.1 | Denitrovibrio acetiphilus | [NiFe] Group 1f | Deferribacteres | Deferribacterales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_013885838.1 | Flexistipes sinusarabici | [NiFe] Group 1f | Deferribacteres | Deferribacterales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_022851572.1 | Geovibrio sp. L21-Ace-BES | [NiFe] Group 1f | Deferribacteres | Deferribacterales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_006562194.1 | Oscillochloris trichoides | [NiFe] Group 1f | Chloroflexi | Chloroflexales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_012121625.1 | Roseiflexus castenholzii | [NiFe] Group 1f | Chloroflexi | Chloroflexales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_011957045.1 | Roseiflexus sp. RS-1 | [NiFe] Group 1f | Chloroflexi | Chloroflexales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_005509950.1 | Corynebacterium amycolatum | [NiFe] Group 1f | Actinobacteria | Actinomycetales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_014310124.1 | Corynebacterium diphtheriae | [NiFe] Group 1f | Actinobacteria | Actinomycetales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_006062526.1 | Corynebacterium durum | [NiFe] Group 1f | Actinobacteria | Actinomycetales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_027012481.1 | Corynebacterium freiburgense | [NiFe] Group 1f | Actinobacteria | Actinomycetales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_005388873.1 | Corynebacterium glucuronolyticum | [NiFe] Group 1f | Actinobacteria | Actinomycetales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_016458088.1 | Corynebacterium pyruviciproducens | [NiFe] Group 1f | Actinobacteria | Actinomycetales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_016422186.1 | Corynebacterium sp. HFH0082 | [NiFe] Group 1f | Actinobacteria | Actinomycetales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_025252525.1 | Corynebacterium vitaeruminis | [NiFe] Group 1f | Actinobacteria | Actinomycetales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_018502767.1 | Frankia sp. BCU110501 | [NiFe] Group 1f | Actinobacteria | Actinomycetales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_018637732.1 | Frankia sp. BMG5.12 | [NiFe] Group 1f | Actinobacteria | Actinomycetales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_020460947.1 | Frankia sp. EAN1pec | [NiFe] Group 1f | Actinobacteria | Actinomycetales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_006544185.1 | Frankia sp. EUN1f | [NiFe] Group 1f | Actinobacteria | Actinomycetales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_004007712.1 | Mobiluncus curtisii | [NiFe] Group 1f | Actinobacteria | Actinomycetales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_004013385.1 | Mobiluncus mulieris | [NiFe] Group 1f | Actinobacteria | Actinomycetales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_022865058.1 | Varibaculum cambriense | [NiFe] Group 1f | Actinobacteria | Actinomycetales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_015898101.1 | Acidobacterium capsulatum | [NiFe] Group 1f | Acidobacteria | Acidobacteriales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
| WP_026441619.1 | Acidobacterium sp. PMMR2 | [NiFe] Group 1f | Acidobacteria | Acidobacteriales | Anaerobic Uptake | Unknown | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Cytochrome b |
Literature
Genetics:
- Coppi, M.V. (2005) The hydrogenases of Geobacter sulfurreducens: a comparative genomic perspective. Microbiol. 151: 1239-1254.
- Greening, C., Biswas, A., Carere, C.R., Jackson, C.J., Taylor, M.C., Stott, M.B., Cook, G.M., 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.
- Leul, M., Normand, P., and Sellstedt, A. (2007) The organization, regulation and phylogeny of uptake hydrogenase genes in Frankia 130: 464-470.
- Richau, K.H., Kudahettige, R.L., Pujic, P., Kudahettige, N.P., and Sellstedt, A. (2013) Structural and gene expression analyses of uptake hydrogenases and other proteins involved in nitrogenase protection in Frankia. J. Biosci. 38, 703-712.
Physiology:
- Mattsson, U., Johansson, L., Sandström, G., and Sellstedt, A. (2001) Frankia KB5 possesses a hydrogenase immunologically related to membrane-bound [NiFe]-hydrogenases. Curr. Microbiol. 42: 438-441.
- Mattsson, U. and Sellstedt, A. (2000) Hydrogenase in Frankia KB5: Expression of and relation to nitrogenase. Can. J. Microbiol. 46: 1091-1095.
- Myers, M.R. and King, G.M. (2016) Isolation and characterization of Acidobacterium ailaaui sp. nov., a novel member of Acidobacteria subdivision 1, from a geothermally heated Hawaiian microbial mat. int. J. Syst. Evol. Microbiol. 66: 5328-5335.
- Takai, K., Kobayashi, H., Nealson, K.H., and Horikoshi, K. (2003). Deferribacter desulfuricans sp. nov., a novel sulfur-, nitrate-and arsenate-reducing thermophile isolated from a deep-sea hydrothermal vent. Int. J. Syst. Evol. Microbiol. 53: 839-846.
- Tremblay, P.L. and Lovley, D.R. (2012) Role of the NiFe hydrogenase Hya in oxidative stress defense in Geobacter sulfurreducens J. Bacteriol. 194: 2248-2253.