[NiFe] Group 2a-hydrogenase

This entry was last updated at: Feb. 9, 2018, 6:36 a.m.

Properties

Group	[NiFe] Group 2: Alternative and sensory H₂-uptake [NiFe] hydrogenases
Subgroup	[NiFe] Group 2a: Cyanobacteria-type
Function	Hydrogenotrophic respiration using O₂ as the terminal electron acceptor. Important for recycling of H₂ produced by nitrogenase and fermentation. Route of electron transfer unresolved.
Activity	H₂-uptake (unidirectional, some high-affinity)
Oxygen tolerance	Some O₂-tolerant
Localisation	Membrane-associated?

Distribution

Ecosystem distribution	Diverse soil and aquatic environments
Taxonomic distribution	Widespread among Cyanobacteria and aerobic soil bacteria (e.g. Actinobacteria)

Genetic Organisation

e.g. Mycobacterium smegmatis (WP_003893634.1):

Architecture

Structures	None
Subunits	3?
Subunit description	None
Catalytic site	[NiFe]-centre
FeS clusters	Proximal: 3Cys1Asn[4Fe4S] Medial: 3Cys[3Fe4S] Distal: 3Cys1Glu[4Fe4S]

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_012536298.1	Acidithiobacillus ferrooxidans	[NiFe] Group 2a	Gammaproteobacteria	Acidithiobacillales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_011603008.1	Frankia alni	[NiFe] Group 2a	Actinobacteria	Actinomycetales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_009739903.1	Frankia sp. QA3	[NiFe] Group 2a	Actinobacteria	Actinomycetales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_006368950.1	Gordonia polyisoprenivorans	[NiFe] Group 2a	Actinobacteria	Actinomycetales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_006335051.1	Gordonia rhizosphera	[NiFe] Group 2a	Actinobacteria	Actinomycetales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_006594684.1	Kineosphaera limosa	[NiFe] Group 2a	Actinobacteria	Actinomycetales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_005626347.1	Mycobacterium hassiacum	[NiFe] Group 2a	Actinobacteria	Actinomycetales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_024444663.1	Mycobacterium iranicum	[NiFe] Group 2a	Actinobacteria	Actinomycetales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_003888964.1	Mycobacterium phlei	[NiFe] Group 2a	Actinobacteria	Actinomycetales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_003893634.1	Mycobacterium smegmatis	[NiFe] Group 2a	Actinobacteria	Actinomycetales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_003925668.1	Mycobacterium thermoresistibile	[NiFe] Group 2a	Actinobacteria	Actinomycetales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_006242868.1	Mycobacterium tusciae	[NiFe] Group 2a	Actinobacteria	Actinomycetales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_011779592.1	Mycobacterium vanbaalenii	[NiFe] Group 2a	Actinobacteria	Actinomycetales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_028656395.1	Nocardioides sp. J54	[NiFe] Group 2a	Actinobacteria	Actinomycetales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_028931752.1	Pseudonocardia asaccharolytica	[NiFe] Group 2a	Actinobacteria	Actinomycetales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_013678342.1	Pseudonocardia dioxanivorans	[NiFe] Group 2a	Actinobacteria	Actinomycetales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_005476263.1	Streptomyces bottropensis	[NiFe] Group 2a	Actinobacteria	Actinomycetales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_013133447.1	Thermobispora bispora	[NiFe] Group 2a	Actinobacteria	Actinomycetales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_012963102.1	Hydrogenobacter thermophilus	[NiFe] Group 2a	Aquificae	Aquificales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_012992443.1	Thermocrinis albus	[NiFe] Group 2a	Aquificae	Aquificales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_029421095.1	Alicyclobacillus macrosporangiidus	[NiFe] Group 2a	Firmicutes	Bacillales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_027417151.1	Aneurinibacillus terranovensis	[NiFe] Group 2a	Firmicutes	Bacillales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_003250668.1	Geobacillus thermoglucosidasius	[NiFe] Group 2a	Firmicutes	Bacillales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_013076467.1	Kyrpidia tusciae	[NiFe] Group 2a	Firmicutes	Bacillales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_028986316.1	Thermicanus aegyptius	[NiFe] Group 2a	Firmicutes	Bacillales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_012615778.1	Chloroflexus aggregans	[NiFe] Group 2a	Chloroflexi	Chloroflexales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_028460308.1	Chloroflexus sp. Y-396-1	[NiFe] Group 2a	Chloroflexi	Chloroflexales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_012122267.1	Roseiflexus castenholzii	[NiFe] Group 2a	Chloroflexi	Chloroflexales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_007308441.1	Crocosphaera watsonii	[NiFe] Group 2a	Cyanobacteria	Chroococcales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_012361536.1	Cyanothece sp. ATCC 51142	[NiFe] Group 2a	Cyanobacteria	Chroococcales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_008275259.1	Cyanothece sp. CCY0110	[NiFe] Group 2a	Cyanobacteria	Chroococcales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_012599193.1	Cyanothece sp. PCC 7424	[NiFe] Group 2a	Cyanobacteria	Chroococcales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_013321766.1	Cyanothece sp. PCC 7822	[NiFe] Group 2a	Cyanobacteria	Chroococcales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_013987182.1	Sulfobacillus acidophilus	[NiFe] Group 2a	Firmicutes	Clostridiales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_009185102.1	Cecembia lonarensis	[NiFe] Group 2a	Bacteroidetes	Cytophagales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_015029646.1	Emticicia oligotrophica	[NiFe] Group 2a	Bacteroidetes	Cytophagales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_026993787.1	Flectobacillus major	[NiFe] Group 2a	Bacteroidetes	Cytophagales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_028526813.1	Runella limosa	[NiFe] Group 2a	Bacteroidetes	Cytophagales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_013921615.1	Runella slithyformis	[NiFe] Group 2a	Bacteroidetes	Cytophagales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_028664870.1	Runella zeae	[NiFe] Group 2a	Bacteroidetes	Cytophagales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_012928387.1	Spirosoma linguale	[NiFe] Group 2a	Bacteroidetes	Cytophagales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_013993526.1	Zobellia galactanivorans	[NiFe] Group 2a	Bacteroidetes	Flavobacteriales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_012681902.1	Gemmatimonas aurantiaca	[NiFe] Group 2a	Gemmatimonadetes	Gemmatimonadales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_053379275.1	Nitrospira moscoviensis	[NiFe] Group 2a	Nitrospirae	Nitrospirales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_015079360.1	Anabaena sp. 90	[NiFe] Group 2a	Cyanobacteria	Nostocales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_011321261.1	Anabaena variabilis	[NiFe] Group 2a	Cyanobacteria	Nostocales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_026092924.1	Calothrix sp. PCC 7103	[NiFe] Group 2a	Cyanobacteria	Nostocales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_006278427.1	Cylindrospermopsis raciborskii	[NiFe] Group 2a	Cyanobacteria	Nostocales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_017656008.1	Microchaete sp. PCC 7126	[NiFe] Group 2a	Cyanobacteria	Nostocales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins
WP_006194531.1	Nodularia spumigena	[NiFe] Group 2a	Cyanobacteria	Nostocales	Aerobic Uptake	Tolerant	5	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	[FeS] protein, hypothetical proteins

Literature

Genetics:

Axelsson, R., Oxelfelt, F., and Lindblad, P. (1999) Transcriptional regulation of Nostoc uptake hydrogenase. FEMS Microbiol. Lett. 170: 77-81.
Berney, M., Greening, C., Hards, K., Collins, D., and Cook, G.M. (2014) Three different [NiFe] hydrogenases confer metabolic flexibility in the obligate aerobe Mycobacterium smegmatis. Environ. Microbiol. 16: 318-330.
Boison, G., Bothe, H., and Schmitz, O. (2000) Transcriptional analysis of hydrogenase genes in the cyanobacteria Anacystis nidulans and Anabaena variabilis monitored by RT-PCR. Curr. Microbiol. 40: 315-321.
Happe, T., Schütz, K., and Böhme, H. (2000) Transcriptional and mutational analysis of the uptake hydrogenase of the filamentous cyanobacterium Anabaena variabilis ATCC 29413. J. Bacteriol. 182: 1624-1631.
Oliveira, P., Leitão, E., Tamagnini, P, Moradas-Ferreira, P., and Oxelfelt, F. (2004) Characterization and transcriptional analysis of hupSLW in Gloeothece sp. ATCC 27152: an uptake hydrogenase from a unicellular cyanobacterium. Microbiol. 150: 3647-3655.
Tamagnini, P., Costa, J.-L., Almeida, L., Oliveira, M.-J., Salema, R., and Lindblad, P. (2000) Diversity of cyanobacterial hydrogenases, a molecular approach. Curr. Microbiol. 40: 356-361.
Tel-Or, E., Luijk, L.W., and Packer, L. (1977) An inducible hydrogenase in cyanobacteria enhances N₂ fixation. FEBS Lett. 78: 49-52.
Vignais, P.M., Billoud, B., and Meyer, J. (2001) Classification and phylogeny of hydrogenases. FEMS Microbiol. Rev. 25: 455-501.

Physiology:

Berney, M., Greening, C., Conrad, R., Jacobs, W.R., and Cook, G.M. (2014) An obligately aerobic soil bacterium activates fermentative hydrogen production to survive reductive stress during hypoxia. Proc. Natl. Acad. Sci. U. S. A. 111: 11479-11484.
Grostern, A. and Alvarez-Cohen, L. (2013) RubisCO-based CO₂ fixation and C1 metabolism in the actinobacterium Pseudonocardia dioxanivorans CB1190. Environ. Microbiol. 15: 3040-3053.
Greening, C., Berney, M., Hards, K., Cook, G.M., and Conrad, R. (2014) A soil actinobacterium scavenges atmospheric H₂ using two membrane-associated, oxygen-dependent [NiFe] hydrogenases. Proc. Natl. Acad. Sci. U. S. A. 111: 4257-61.
Hedrich, S. and Johnson, D.B. (2013) Aerobic and anaerobic oxidation of hydrogen by acidophilic bacteria. FEMS Microbiol. Lett. 349: 40-45.
Houchins, J.P. and Burris, R.H. (1981) Occurrence and localization of two distinct hydrogenases in the heterocystous cyanobacterium Anabaena sp. strain 7120. J. Bacteriol. 146: 209-214.
Koch et al. (2014) Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation. Science 345: 1052-1054.
Lindberg, P., Schütz, K., Happe, T., and Lindblad, P. (2002) A hydrogen-producing, hydrogenase-free mutant strain of Nostoc punctiforme ATCC 29133. Int. J. Hydrogen Energy 27: 1291-1296.
Masukawa, H., Mochimaru, M., and Sakurai, H. (2002) Disruption of the uptake hydrogenase gene, but not of the bidirectional hydrogenase gene, leads to enhanced photobiological hydrogen production by the nitrogen-fixing cyanobacterium Anabaena sp. PCC 7120. Appl. Microbiol. Biotechnol. 58: 618-624.
Mori, J.F., Scott, J.J., Hager, K.W., Moyer, C.L., Küsel, K., and Emerson, D. (2017) Physiological and ecological implications of an iron-or hydrogen-oxidizing member of the Zetaproteobacteria, Ghiorsea bivora, gen. nov., sp. nov. ISME J. 11: 2624-2636.
Ohmura, N., Sasaki, K., Matsumoto, N. and Saiki, H. (2002) Anaerobic respiration using Fe³⁺, S₀, and H₂ in the chemolithoautotrophic bacterium Acidithiobacillus ferrooxidans. J. Bacteriol. 184: 2081-2087.
Papen, H., Kentemich, T., Schmülling, T., and Bothe, H. (1986) Hydrogenase activities in cyanobacteria. Biochimie 68: 121-132.
Shima, S. and Suzuki, K. (1993) Hydrogenobacter acidophilus sp. nov., a thermoacidophilic, aerobic, hydrogen-oxidizing bacterium requiring elemental sulfur for growth. Int. J. Syst. Bacteriol. 43: 703-708.

Biochemistry:

Kumazawa, S. and Mitsui, A. (1985) Comparative amperometric study of uptake hydrogenase and hydrogen photoproduction between heterocystous cyanobacterium Anabaena cylindrica B629 and nonheterocystous cyanobacterium Oscillatoria sp. strain Miami BG7. Appl. Environ. Microbiol. 50: 287-291.
Raleiras, P., Kellers, P., Lindblad, P., Styring, S. and Magnuson, A. (2013) Isolation and characterization of the small subunit of the uptake hydrogenase from the cyanobacterium Nostoc punctiforme. J. Biol. Chem. 288: 18345-18352.
Raleiras, P., Khanna, N., Miranda, H., Mészáros, L.S., Krassen, H., Ho, F., Battchikova, N., Aro, E.M., Magnuson, A., Lindblad, P., and Styring, S (2016) Turning around the electron flow in an uptake hydrogenase. EPR spectroscopy and in vivo activity of a designed mutant in HupSL from Nostoc punctiforme. Energy Environ. Sci. 9: 581-594.

Chemistry:

Bleijlevens, B., Jongh, T.E., Chen, Z., Li, T., Fischer, J.R., Förster, J., Friedrich, C.G., Bagley, K.A., Albracht, S.P., and Lubitz, W. (2007) Characterization of a cyanobacterial-like uptake [NiFe]- hydrogenase: EPR and FTIR spectroscopic studies of the enzyme from Acidithiobacillus ferrooxidans. J. Biol. Inorg. Chem. 12: 212-233.