[NiFe] Group 2d-hydrogenase

This entry was last updated at: Feb. 9, 2018, 7:09 a.m.

Properties

Group	[NiFe] Group 2: Alternative and sensory H₂-uptake [NiFe] hydrogenases
Subgroup	[NiFe] Group 2d: Aquificae-type
Function	Unresolved role. Enzyme may generate reductant for carbon fixation, support hydrogenotrophic sulfur respiration, or have a regulatory role.
Activity	H₂-uptake (unidirectional)?
Oxygen tolerance	O₂-tolerant?
Localisation	Cytosolic?

Distribution

Ecosystem distribution	In low abundance in hot spring samples
Taxonomic distribution	Exclusive to Aquificae and Epsilonproteobacteria

Genetic Organisation

e.g. Aquifex aeolicus (WP_010880487.1):

Architecture

Structures	None
Subunits	2?
Subunit description	HuaL (hydrogenase large subunit) HuaS (hydrogenase small subunit) Some appear to be transcribed with helix-turn-helix proteins
Catalytic site	[NiFe]-centre
FeS clusters	Proximal: 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.

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_010880487.1	Aquifex aeolicus	[NiFe] Group 2d	Aquificae	Aquificales	Anaerobic Uptake	Unknown	2	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	None
WP_008286852.1	Hydrogenivirga sp. 128-5-R1-1	[NiFe] Group 2d	Aquificae	Aquificales	Anaerobic Uptake	Unknown	2	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	None
WP_012963643.1	Hydrogenobacter thermophilus	[NiFe] Group 2d	Aquificae	Aquificales	Anaerobic Uptake	Unknown	2	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	None
WP_012514441.1	Hydrogenobaculum sp. Y04AAS1	[NiFe] Group 2d	Aquificae	Aquificales	Anaerobic Uptake	Unknown	2	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	None
WP_012676217.1	Persephonella marina	[NiFe] Group 2d	Aquificae	Aquificales	Anaerobic Uptake	Unknown	2	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	None
WP_029520218.1	Persephonella sp. IF05-L8	[NiFe] Group 2d	Aquificae	Aquificales	Anaerobic Uptake	Unknown	2	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	None
WP_029523037.1	Persephonella sp. KM09-Lau-8	[NiFe] Group 2d	Aquificae	Aquificales	Anaerobic Uptake	Unknown	2	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	None
WP_012673603.1	Sulfurihydrogenibium azorense	[NiFe] Group 2d	Aquificae	Aquificales	Anaerobic Uptake	Unknown	2	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	None
WP_028949944.1	Sulfurihydrogenibium subterraneum	[NiFe] Group 2d	Aquificae	Aquificales	Anaerobic Uptake	Unknown	2	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	None
WP_012992449.1	Thermocrinis albus	[NiFe] Group 2d	Aquificae	Aquificales	Anaerobic Uptake	Unknown	2	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	None
WP_025306143.1	Thermocrinis ruber	[NiFe] Group 2d	Aquificae	Aquificales	Anaerobic Uptake	Unknown	2	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	None
WP_020848144.1	Arcobacter butzleri	[NiFe] Group 2d	Epsilonproteobacteria	Campylobacterales	Anaerobic Uptake	Unknown	2	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	None
WP_013135162.1	Arcobacter nitrofigilis	[NiFe] Group 2d	Epsilonproteobacteria	Campylobacterales	Anaerobic Uptake	Unknown	2	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	None
WP_013460910.1	Sulfuricurvum kujiense	[NiFe] Group 2d	Epsilonproteobacteria	Campylobacterales	Anaerobic Uptake	Unknown	2	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	None
WP_015654358.1	Sulfuricurvum sp. RIFRC-1	[NiFe] Group 2d	Epsilonproteobacteria	Campylobacterales	Anaerobic Uptake	Unknown	2	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	None
WP_011373066.1	Sulfurimonas denitrificans	[NiFe] Group 2d	Epsilonproteobacteria	Campylobacterales	Anaerobic Uptake	Unknown	2	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	None
WP_008339288.1	Sulfurimonas gotlandica	[NiFe] Group 2d	Epsilonproteobacteria	Campylobacterales	Anaerobic Uptake	Unknown	2	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	None
WP_025344558.1	Sulfurospirillum multivorans	[NiFe] Group 2d	Epsilonproteobacteria	Campylobacterales	Anaerobic Uptake	Unknown	2	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	None
WP_007473987.1	Caminibacter mediatlanticus	[NiFe] Group 2d	Epsilonproteobacteria	Nautiliales	Anaerobic Uptake	Unknown	2	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	None
WP_024789023.1	Lebetimonas sp. JH292	[NiFe] Group 2d	Epsilonproteobacteria	Nautiliales	Anaerobic Uptake	Unknown	2	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	None
WP_024786773.1	Lebetimonas sp. JH369	[NiFe] Group 2d	Epsilonproteobacteria	Nautiliales	Anaerobic Uptake	Unknown	2	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	None
WP_012663437.1	Nautilia profundicola	[NiFe] Group 2d	Epsilonproteobacteria	Nautiliales	Anaerobic Uptake	Unknown	2	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	None
WP_013553042.1	Nitratifractor salsuginis	[NiFe] Group 2d	Epsilonproteobacteria	Nautiliales	Anaerobic Uptake	Unknown	2	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	None

Literature

Genetics:

Deckert, G. et al. (1998) The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature 392: 353-358.
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.
Kruse, S., Goris, T., Wolf, M., Wei, X., and Diekert, G. (2017). The NiFe hydrogenases of the tetrachloroethene-respiring Epsilonproteobacterium Sulfurospirillum multivorans: biochemical studies and transcription analysis. Front. Microbiol. 8: 444.
Ueda, Y., Yamamoto, M., Urasaki, T., Arai, H., Ishii, M., and Igarashi, Y. (2007) Sequencing and reverse transcription-polymerase chain reaction (RT-PCR) analysis of four hydrogenase gene clusters from an obligately autotrophic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus TK-6. J. Biosci. Bioeng. 104: 470-475.

Physiology:

Brugna-Guiral, M, Tron, P, Nitschke, W., Stetter, K.-O., Burlat, B., Guigliarelli, B, Bruschi, M., and Giudici-Orticoni, M.T. (2003) [NiFe] hydrogenases from the hyperthermophilic bacterium Aquifex aeolicus: properties, function, and phylogenetics. Extremophiles 7: 147-157.
Guiral, M., Aubert, C., and Giudici-Orticoni, M.T. (2005) Hydrogen metabolism in the hyperthermophilic bacterium Aquifex aeolicus. Biochem. Soc. Trans. 33, 22-24.
Guiral, M., Tron, P., Belle, V., Aubert, C., Léger, C., Guigliarelli, B., Giudici-Orticoni, M.T. (2006) Hyperthermostable and oxygen resistant hydrogenases from a hyperthermophilic bacterium Aquifex aeolicus: physicochemical properties. Int. J. Hydrogen Energy 31: 1424-1431.