[NiFe] Group 1e-hydrogenase

This entry was last updated at: Feb. 9, 2018, 5:41 a.m.

Properties

Group	[NiFe] Group 1: Respiratory H₂-uptake [NiFe] hydrogenases
Subgroup	[NiFe] Group 1e: Isp-type
Function	Hydrogenotrophic respiration using sulfur as terminal electron acceptor. Route of electron transfer unresolved. Complex can also evolve H₂ using sulfur-derived electrons possibly through reversed electron flow or electron-bifurcation.
Activity	Bidirectional (possibly electron-bifurcating)
Oxygen tolerance	O₂-sensitive (some tolerance in microoxic conditions)
Localisation	Membrane-bound

Distribution

Ecosystem distribution	Soil and aquatic systems with high sulfur content
Taxonomic distribution	Present in phototrophic and chemotrophic bacteria capable of respiratory sulfur oxidation and reduction

Genetic Organisation

e.g. Allochromatium vinosum (WP_012971230.1):

Architecture

Structures	3MYR (Allochromatium vinosum, 2.1 Å resolution, inactive)
Subunits	4
Subunit description	None
Catalytic site	[NiFe]-centre
FeS clusters	Proximal: 4Cys[4Fe4S] Medial: 3Cys[3Fe4S] Distal: 3Cys1His[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_012537694.1	Acidithiobacillus ferrooxidans	[NiFe] Group 1e	Gammaproteobacteria	Acidithiobacillales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_015066016.1	Alteromonas macleodii	[NiFe] Group 1e	Gammaproteobacteria	Alteromonadales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_006991846.1	Glaciecola mesophila	[NiFe] Group 1e	Gammaproteobacteria	Alteromonadales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_013755279.1	Glaciecola sp. 4H-3-7+YE-5	[NiFe] Group 1e	Gammaproteobacteria	Alteromonadales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_029133715.1	Sedimenticola selenatireducens	[NiFe] Group 1e	Gammaproteobacteria	Alteromonadales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_010880593.1	Aquifex aeolicus	[NiFe] Group 1e	Aquificae	Aquificales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_008287448.1	Hydrogenivirga sp. 128-5-R1-1	[NiFe] Group 1e	Aquificae	Aquificales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_012962745.1	Hydrogenobacter thermophilus	[NiFe] Group 1e	Aquificae	Aquificales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_012992451.1	Thermocrinis albus	[NiFe] Group 1e	Aquificae	Aquificales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_012971230.1	Allochromatium vinosum	[NiFe] Group 1e	Gammaproteobacteria	Chromatiales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_020503980.1	Lamprocystis purpurea	[NiFe] Group 1e	Gammaproteobacteria	Chromatiales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_020508075.1	Lamprocystis purpurea	[NiFe] Group 1e	Gammaproteobacteria	Chromatiales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_015258842.1	Thioalkalivibrio nitratireducens	[NiFe] Group 1e	Gammaproteobacteria	Chromatiales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_018952796.1	Thioalkalivibrio sp. ALJ17	[NiFe] Group 1e	Gammaproteobacteria	Chromatiales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_026340838.1	Thioalkalivibrio sp. ALJT	[NiFe] Group 1e	Gammaproteobacteria	Chromatiales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_012637835.1	Thioalkalivibrio sulfidiphilus	[NiFe] Group 1e	Gammaproteobacteria	Chromatiales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_007191025.1	Thiocapsa marina	[NiFe] Group 1e	Gammaproteobacteria	Chromatiales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
AAC38282.1	Thiocapsa roseopersicina	[NiFe] Group 1e	Gammaproteobacteria	Chromatiales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_014779054.1	Thiocystis violascens	[NiFe] Group 1e	Gammaproteobacteria	Chromatiales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_014777800.1	Thiocystis violascens	[NiFe] Group 1e	Gammaproteobacteria	Chromatiales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_015279763.1	Thioflavicoccus mobilis	[NiFe] Group 1e	Gammaproteobacteria	Chromatiales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_015282140.1	Thioflavicoccus mobilis	[NiFe] Group 1e	Gammaproteobacteria	Chromatiales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_007039064.1	Thiorhodococcus drewsii	[NiFe] Group 1e	Gammaproteobacteria	Chromatiales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_007039027.1	Thiorhodococcus drewsii	[NiFe] Group 1e	Gammaproteobacteria	Chromatiales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_006786088.1	Thiorhodospira sibirica	[NiFe] Group 1e	Gammaproteobacteria	Chromatiales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_009147062.1	Thiorhodovibrio sp. 970	[NiFe] Group 1e	Gammaproteobacteria	Chromatiales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_013029748.1	Sideroxydans lithotrophicus	[NiFe] Group 1e	Betaproteobacteria	Gallionellales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_018077111.1	Thiobacillus denitrificans	[NiFe] Group 1e	Betaproteobacteria	Hydrogenophilales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_018508052.1	Thiobacillus thioparus	[NiFe] Group 1e	Betaproteobacteria	Hydrogenophilales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_008030254.1	Rhodobacter sp. SW2	[NiFe] Group 1e	Alphaproteobacteria	Rhodobacterales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_018610610.1	Uliginosibacterium gangwonense	[NiFe] Group 1e	Betaproteobacteria	Rhodocyclales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_002684413.1	Beggiatoa alba	[NiFe] Group 1e	Gammaproteobacteria	Thiotrichales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_028490337.1	Thiothrix lacustris	[NiFe] Group 1e	Gammaproteobacteria	Thiotrichales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein
WP_002706902.1	Thiothrix nivea	[NiFe] Group 1e	Gammaproteobacteria	Thiotrichales	Anaerobic Uptake	Sensitive	4	[NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster	Cytochrome b, [FeS] protein

Literature

Genetics:

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.
Kovács, Á, Rákhley, G., Browning, D.F., Fülöp, A., Maróti, G., Busby, S.J.W., and Kovács, K.L. (2005) An FNR-type regulator controls the anaerobic expression of Hyn hydrogenase in Thiocapsa roseopersicina. J. Bacteriol. 187: 2618-2627.
Pandelia, M.E., Lubitz, W., and Nitschke, W. (2012) Evolution and diversification of Group 1 [NiFe] hydrogenases. Is there a phylogenetic marker for O₂-tolerance? BBA Bioenergetics 1817: 1565-1575.
Rákhely, G., Colbeau, A., Garin, J., Vignais, P.M. and Kovács, K.L. (1998) Unusual organization of the genes coding for HydSL, the stable [NiFe] hydrogenase in the photosynthetic bacterium Thiocapsa roseopersicina BBS. J. Bacteriol. 180: 1460-1465.

Physiology:

Kávacs, K.L., Kávacs, A.T., Maroti, G., Meszaros, L.S., Balogh, J., Latinovics, D., Fülöp, A., David, R., Doroghazi, E., and Rákhely, G. (2005) The hydrogenases of Thiocapsa roseopersicina. Biochem. Soc. Trans. 33: 61-63.
Pálágyi-Mészáros, L.S., Maróti, J., Latinovics, D., Balogh, T., Klement, E., Medzihradszky, K.F., Rákhely, G., and Kovács, K.L. (2009) Electron-transfer subunits of the NiFe hydrogenases in Thiocapsa roseopersicina BBS. FEBS J. 276: 164-174.
Laurinavichene, T.V., Rákhley, G., Kovács, K.L., and Tsygankov, A.A. (2007) The effect of sulfur compounds on H₂ evolution/consumption reactions, mediated by various hydrogenases, in the purple sulfur bacterium, Thiocapsa roseopersicina. Arch. Microbiol. 188: 403-410.
Tengölics, R., Mészáros, L., Györi, E., Doffkay, Z., Kovács, K., and Rákhely, G. (2014). Connection between the membrane electron transport system and Hyn hydrogenase in the purple sulfur bacterium, Thiocapsa roseopersicina BBS. BBA Bioenergetics 1837: 1691-1698.
Weissgerber, T., Sylvester, M., Kröninger, L., and Dahl, C. (2014) A comparative quantitative proteomic study identifies new proteins relevant for sulfur oxidation in the purple sulfur bacterium Allochromatium vinosum. Appl. Environ. Microbiol. 80: 2279-2292.

Biochemistry:

Gitlitz, P.H. and Krasna, A.I. (1975) Structural and catalytic properties of hydrogenase from Chromatium. Biochem.: 14: 2561-2568.
Kakuno, T., Kaplan, N.O. and Kamen, M.D., 1977. Chromatium hydrogenase. Proc. Natl. Acad. Sci. USA 74: 861-863.
Léger, C., Jones, A.K., Roseboom, W., Albracht, S.P.J., and Armstrong, F.A. (2002) Enzyme electrokinetics: hydrogen evolution and oxidation by Allochromatium vinosum [NiFe]-hydrogenase. Biochem. 41: 15736-15746.
Kellers, P., Ogata, H., and Lubitz, W. (2008) Purification, crystallization and preliminary X-ray analysis of the membrane-bound [NiFe] hydrogenase from Allochromatium vinosum. Acta Crystallogr. F. Struct. Biol. Cryst. Commun. 64: 719-722.
Ogata, H., Kellers, P., and Lubitz, W. (2010) The crystal structure of the [NiFe] hydrogenase from the photosynthetic bacterium Allochromatium vinosum: characterization of the oxidized enzyme (Ni-A state). J. Mol. Biol. 402: 428-444.
Vargas, W.A., Weyman, P.D., Tong, Y.K., Smith, H.O., and Xu, Q. (2011). [NiFe] hydrogenase from Alteromonas macleodii with unusual stability in the presence of oxygen and high temperature. Appl. Environ. Microbiol. 77: 1990-1998.
Weyman, P.D., Vargas, W.A., Tong, Y., Yu, J. Maness, P.-C., Smith, H.O., and Xu, Q. (2011). Heterologous expression of Alteromonas macleodii and Thiocapsa roseopersicina [NiFe]-hydrogenases in Synechococcus elongatus. PLOS One 6: e20126.

Chemistry:

Albracht, S.P.J., Kalkman, M.L., and Slater, E.C., 1983. Magnetic interaction of nickel(III) and the iron-sulphur cluster in hydrogenase from Chromatium vinosum. BBA Bioenergetics 724: 309-316.
Bagley, K.A., Duin, E.C., Roseboom, W., Albracht, S.P., and Woodruff, W.H. (1995) Infrared-detectable group senses changes in charge density on the nickel center in hydrogenase from Chromatium vinosum. Biochem. 34: 5527-5535.
Bagley, K.A., Van Garderen, C.J., Chen, M., Woodruff, W.H., Duin, E.C., and Albracht, S.P. (1994) Infrared studies on the interaction of carbon monoxide with divalent nickel in hydrogenase from Chromatium vinosum. Biochem. 33: 9229-9236.
Bleijlevens, B., Faber, B.W., and Albracht, S.P. (2001) The [NiFe] hydrogenase from Allochromatium vinosum studied in EPR-detectable states: H/D exchange experiments that yield new information about the structure of the active site. J. Biol. Inorg. Chem. 6: 763-769.
Bleijlevens, B., van Broekhuizen, F.A., de Lacey, A.L., Roseboom, W., Fernandez, V.M., and Albracht, S.P.J. (2004) The activation of the [NiFe]-hydrogenase from Allochromatium vinosum. An infrared spectro-electrochemical study. J. Biol. Inorg. Chem. 9: 743-752.
Breglia, R., Greco, C., Fantucci, P., de Gioia, L., and Bruschi, M. (2017) Theoretical investigation of aerobic and anaerobic oxidative inactivation of the [NiFe]-hydrogenase active site. Phys. Chem. Chem. Phys. 20: 1693-1706.
Coremans, J.M.C.C., Vangarderen, C.J., and Albracht, S.P.J. (1992) On the redox equilibrium between H₂ and hydrogenase. Biochim. Biophys. Acta 1119: 148-156.
Coremans, J.M.C.C., Van der Zwaan, J.W. and Albracht, S.P.J. (1992) Distinct redox behaviour of prosthetic groups in ready and unready hydrogenase from Chromatium vinosum. BBA Protein Struct. Mol. Enzymol. 1119: 157-168.
Davidson, G., Choudhury, S.B., Gu, Z., Bose, K., Roseboom, W., Albracht, S.P., and Maroney, M.J. (2000) Structural examination of the nickel site in Chromatium vinosum hydrogenase: redox state oscillations and structural changes accompanying reductive activation and CO binding. Biochem. 39: 7468-7479.
George, S.J., Kurkin, S., Thorneley, R.N.F., and Albracht, S.P.J. (2004) Reactions of H₂, CO, and O₂ with active [NiFe]-hydrogenase from Allochromatium vinosum. A stopped-flow infrared study. Biochem. 43: 6808-6819.
Happe, R.P., Roseboom, W., and Albracht, S.P., (1999). Pre-steady-state kinetics of the reactions of [NiFe]-hydrogenase from Chromatium vinosum with H₂ and CO. Eur. J. Biochem., 259: 602-608.
Jones, A.K., Lamle, S.E., Pershad, H.R., Vincent, K.A., Albracht, S.P.J., and Armstrong, F.A. (2003) Enzyme electrokinetics: Electrochemical studies of the anaerobic interconversions between active and inactive states of Allochromatium vinosum [NiFe]-hydrogenase. J. Am. Chem. Soc. 125: 8505-8514.
Kurkin, S., George, S.J., Thorneley, R.N.F., and Albracht, S.P.J. (2004). Hydrogen-induced activation of the [NiFe]-hydrogenase from Allochromatium vinosum as studied by stopped-flow infrared spectroscopy. Biochem. 43: 6820-6831.
Lamle, S.E., Albracht, S.P.J., and Armstrong, F.A. (2004) Electrochemical potential-step investigations of the aerobic interconversions of [NiFe]-hydrogenase from Allochromatium vinosum: insights into the puzzling difference between unready and ready oxidized inactive states. J. Am. Chem. Soc. 126: 14899-14909.
Pershad, H.R., Duff, J.L., Heering, H.A., Duin, E.C., Albracht, S.P., and Armstrong, F.A. (1999) Catalytic electron transport in Chromatium vinosum [NiFe]-hydrogenase: application of voltammetry in detecting redox-active centers and establishing that hydrogen oxidation is very fast even at potentials close to the reversible H⁺/H₂ value. Biochem. 38: 8992-8999.
Surerus, K.K., Chen, M., van der Zwaan, J.W., Rusnak, F.M., Kolk, M., Duin, E.C., Albracht, S.P., and Muenck, E. (1994) Further characterization of the spin coupling observed in oxidized hydrogenase from Chromatium vinosum. A Mössbauer and multifrequency EPR study. Biochem. 33: 4980-4993.
Van der Zwaan, J.W., Albracht, S.P.J., Fontijn, R.D., and Slater, E.C. (1985) Monovalent nickel in hydrogenase from Chromatium vinosum. FEBS Lett. 179: 271-277.
Van der Zwaan, J.W., Albracht, S.P.J., Fontijn, R.D., and Roelofs, Y.B.M. (1986) EPR evidence for direct interaction of carbon monoxide with nickel in hydrogenase from Chromatium vinosum. BBA Protein Struct. Mol. Enzymol. 872: 208-215.
Van der Zwaan, J.W., Coremans, J.M.C.C., Bouwens, E.C.M., and Albracht, S.P.J. (1990) Effect of ¹⁷O₂ and ¹³CO on EPR espectra of nickel in hydrogenase from Chromatium vinosum. BBA Protein Struct. Mol. Enzymol. 1041: 101-110.