[NiFe] Group 2b-hydrogenase

This entry was last updated at: June 13, 2016, 11:11 a.m.

Properties

Group	[NiFe] Group 2: Alternative and sensory H₂-uptake [NiFe] hydrogenases
Subgroup	[NiFe] Group 2b: Histidine kinase-linked
Function	H₂-sensing in regulatory cascades. Enzyme transfers H₂-liberated electrons to PAS domain. Associated redox change modulates histidine kinase activity and in turn the two-component system controlling expression of primary H₂-uptake hydrogenases.
Activity	H₂-sensing
Oxygen tolerance	O₂-tolerant
Localisation	Cytosolic

Distribution

Ecosystem distribution	Various soil and aquatic samples
Taxonomic distribution	Exclusive to aerobic Proteobacteria

Genetic Organisation

e.g. Ralstonia eutropha (WP_011153946.1):

Architecture

Structures	None
Subunits	3
Subunit description	HupV (hydrogenase large subunit) HupU (hydrogenase small subunit) HupK (histidine kinase) Interacts with response regulator (HupR)
Catalytic site	[NiFe]-centre
FeS clusters	Proximal: 4Cys[4Fe4S] Medial: 4Cys[4Fe4S] 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)
AAB49361.1	Alcaligenes hydrogenophilus	[NiFe] Group 2b	Betaproteobacteria	Burkholderiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
AAX40740.1	Thiocapsa roseopersicina	[NiFe] Group 2b	Gammaproteobacteria	Chromatiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_002706876.1	Thiothrix nivea	[NiFe] Group 2b	Gammaproteobacteria	Thiotrichales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_002720656.1	Rhodobacter sphaeroides	[NiFe] Group 2b	Alphaproteobacteria	Rhodobacterales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_003612204.1	Methylosinus trichosporium	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_004274639.1	Azospirillum amazonense	[NiFe] Group 2b	Alphaproteobacteria	Rhodospiralles	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_005863651.1	Sagittula stellata	[NiFe] Group 2b	Alphaproteobacteria	Rhodobacterales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_007041639.1	Thiorhodococcus drewsii	[NiFe] Group 2b	Gammaproteobacteria	Chromatiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_007194465.1	Thiocapsa marina	[NiFe] Group 2b	Gammaproteobacteria	Chromatiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_007796497.1	Pelagibaca bermudensis	[NiFe] Group 2b	Alphaproteobacteria	Rhodobacterales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_008030826.1	Rhodobacter sp. SW2	[NiFe] Group 2b	Alphaproteobacteria	Rhodobacterales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_008068222.1	Novosphingobium nitrogenifigens	[NiFe] Group 2b	Alphaproteobacteria	Sphingomonadales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_008282513.1	Roseovarius sp. TM1035	[NiFe] Group 2b	Alphaproteobacteria	Rhodobacterales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_008386856.1	Rhodovulum sp. PH10	[NiFe] Group 2b	Alphaproteobacteria	Rhodobacterales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_008622301.1	Magnetospirillum sp. SO-1	[NiFe] Group 2b	Alphaproteobacteria	Rhodospiralles	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_008886444.1	Citreicella sp. SE45	[NiFe] Group 2b	Alphaproteobacteria	Rhodobacterales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_009505605.1	Citreicella sp. 357	[NiFe] Group 2b	Alphaproteobacteria	Rhodobacterales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_009566015.1	Rhodobacter sp. AKP1	[NiFe] Group 2b	Alphaproteobacteria	Rhodobacterales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_010563032.1	Pseudomonas extremaustralis	[NiFe] Group 2b	Gammaproteobacteria	Pseudomonadales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_011089681.1	Bradyrhizobium diazoefficiens	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_011153946.1	Ralstonia eutropha	[NiFe] Group 2b	Betaproteobacteria	Burkholderiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_011384345.1	Magnetospirillum magneticum	[NiFe] Group 2b	Alphaproteobacteria	Rhodospiralles	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_011466381.1	Rhodoferax ferrireducens	[NiFe] Group 2b	Betaproteobacteria	Burkholderiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_011629746.1	Alkalilimnicola ehrlichii	[NiFe] Group 2b	Gammaproteobacteria	Chromatiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_011662668.1	Rhodopseudomonas palustris	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_011714112.1	Magnetococcus marinus	[NiFe] Group 2b	Alphaproteobacteria	Magnetococcales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_011749363.1	Paracoccus denitrificans	[NiFe] Group 2b	Alphaproteobacteria	Rhodobacterales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_011767530.1	Azoarcus sp. BH72	[NiFe] Group 2b	Betaproteobacteria	Rhodocyclales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_011801344.1	Polaromonas naphthalenivorans	[NiFe] Group 2b	Betaproteobacteria	Burkholderiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_011830389.1	Methylibium petroleiphilum	[NiFe] Group 2b	Betaproteobacteria	Burkholderiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_011880080.1	Burkholderia vietnamiensis	[NiFe] Group 2b	Betaproteobacteria	Burkholderiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_011996000.1	Xanthobacter autotrophicus	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_012169127.1	Azorhizobium caulinodans	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_012384146.1	Beijerinckia indica	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_012976476.1	Azospirillum lipoferum	[NiFe] Group 2b	Alphaproteobacteria	Rhodospiralles	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_013124503.1	Thiomonas intermedia	[NiFe] Group 2b	Betaproteobacteria	Burkholderiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_013418661.1	Rhodomicrobium vannielii	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_013913763.1	Oligotropha carboxidovorans	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_014429792.1	Rubrivivax gelatinosus	[NiFe] Group 2b	Betaproteobacteria	Burkholderiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_014725822.1	Burkholderia sp. KJ006	[NiFe] Group 2b	Betaproteobacteria	Burkholderiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_014891818.1	Methylocystis sp. SC2	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_015437371.1	Azoarcus sp. KH32C	[NiFe] Group 2b	Betaproteobacteria	Rhodocyclales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_015597392.1	Hyphomicrobium denitrificans	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_015668919.1	Bradyrhizobium oligotrophicum	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_017845586.1	Pseudomonas veronii	[NiFe] Group 2b	Gammaproteobacteria	Pseudomonadales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_018266917.1	Methylosinus sp. LW4	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_018391446.1	Ancylobacter sp. FA202	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_018412518.1	Methyloversatilis sp. NVD	[NiFe] Group 2b	Betaproteobacteria	Rhodocyclales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_018904285.1	Variovorax paradoxus	[NiFe] Group 2b	Betaproteobacteria	Burkholderiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_019574255.1	Curvibacter lanceolatus	[NiFe] Group 2b	Betaproteobacteria	Burkholderiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator

Literature

Genetics:

Black, L.K., Fu, C., and Maier, R.J. (1994) Sequences and characterization of hupU and hupV genes of Bradyrhizobium japonicum encoding a possible nickel-sensing complex involved in hydrogenase expression. J. Bacteriol. 176: 7102-7106.
Colbeau, A. and Vignais, P.M. (1992) Use of hupS::lacZ gene fusion to study regulation of hydrogenase expression in Rhodobacter capsulatus: stimulation by H₂. J. Bacteriol. 172: 4258-4264.
Dischert, W., Vignais, P.M., and Colbeau, A. (1999) The synthesis of Rhodobacter capsulatus HupSL hydrogenase is regulated by the two-component HupT/HupR system. Mol. Microbiol. 34: 995-1006
Elsen, S., Colbeau, A., Chabert, J., and Vignais, P.M. (1996) The hupTUV operon is involved in negative control of hydrogenase synthesis in Rhodobacter capsulatus. J. Bacteriol. 178: 5174-5181.
Prosser, J., Graham, L., and Maier, R.J. (1988) Hydrogen-mediated enhancement of hydrogenase expression in Azotobacter vinelandii. J. Bacteriol. 170: 1990-1993.
Rey, F.E., Oda, Y. and Harwood, C.S. (2006) Regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in Rhodopseudomonas palustris. J. Bacteriol. 188: 6143-6152.
Schwartz, E., Buhrke, T., Gerischer, U., and Friedrich, B. (1999) Positive transcriptional feedback controls hydrogenase expression in Alcaligenes eutrophus hydrogenase genes. J. Bacteriol. 181: 5684-5692.
Schwartz, E., Gerischer, U., and Friedrich, B. (1998) Transcriptional regulation of Alcaligenes eutrophus hydrogenase genes. J. Bacteriol. 180: 3197-3204.
Vignais, P.M., Billoud, B., and Meyer, J. (2001) Classification and phylogeny of hydrogenases. FEMS Microbiol. Rev. 25: 455-501.
Lenz, O., Stack, A., Tran-Betcke, A., Friedrich, B. (1997) A hydrogen-sensing system in transcriptional regulation of hydrogenase gene expression in Alcaligenes species. J. Bacteriol. 179: 1655-1663.

Physiology:

Friedrich, B., Buhrke, T., Burgdorf, T., and Lenz, O. (2005) A hydrogen-sensing multiprotein complex controls aerobic hydrogen metabolism in Ralstonia eutropha. Biochem. Soc. Trans. 33: 97-101.
Greening, C. and Cook, G. (2014) Integration of hydrogenase expression and hydrogen sensing in bacterial cell physiology. Curr. Opin. Microbiol. 18: 30-38.
Kleihues, L., Lenz, O., Bernhard, M., Buhrke, T., and Friedrich, B. (2000) The H₂ sensor of Ralstonia eutropha is a member of the subclass of regulatory [NiFe]-hydrogenases. J. Bacteriol. 182: 2716-2724.
Lenz, O. and Friedrich, B. (1998). A novel multicomponent regulatory system mediates H₂ sensing in Alcaligenes eutrophus. Proc. Acad. Natl. Sci. U.S.A. 95: 12474-12479.

Biochemistry:

Bernhard, M., Buhrke, T., Bleijlevens, B., de Lacey, A.L., Fernandez, V.M., Albracht, S.P., and Friedrich, B. (2001) The H₂ sensor of Ralstonia eutropha. Biochemical characteristics, spectroscopic properties, and its interaction with a histidine kinase. J. Biol. Chem. 276: 15592-15597.
Buhrke, T., Lenz, O., Krauss, N., and Friedrich, B. (2005) Oxygen tolerance of the H₂-sensing [NiFe] hydrogenase from Ralstonia eutropha H16 is based on limited access of oxygen to the active site. J. Biol. Chem. 280: 23791-23796.
Buhrke, T., Lenz, O., Porthun, A., and Friedrich, B. (2004). The H₂-sensing complex of Ralstonia eutropha: interaction between a regulatory [NiFe] hydrogenase and a histidine kinase. Mol. Microbiol. 51: 1677-1689.
Duché, O, Elsen, S., Cournac, L., and Colbeau, A. (2005) Enlarging the gas access channel to the active site renders the regulatory hydrogenase HupUV of Rhodobacter capsulatus O₂ sensitive without affecting its transductory activity. FEBS J. 272: 3899-3908.
Elsen, S., Duché, O., and Colbeau, A. (2003) Interaction between the H₂ sensor HupUV and the histidine kinase HupT controls HupSL hydrogenase synthesis in Rhodobacter capsulatus. J. Bacteriol. 185: 7111-7119.
Gebler, A., Burgdorf, T., de Lacey, A.L., Rüdiger, O., Martinez-Arias, A., Lenz, O., and Friedrich, B. (2007) Impact of alterations near the [NiFe] active site on the function of the H₂ sensor from Ralstonia eutropha. FEBS J. 274: 74-85.

Chemistry

Ash, P.A., Liu, J., Coutard, N., Heidary, N., Horch, M., Gudim, I., Simler, T., Zebger, I., Lenz, O., and Vincent, K.A. (2015) Electrochemical and infrared spectroscopic studies provide insight into reactions of the NiFe regulatory hydrogenase from Ralstonia eutropha with O₂ and CO. J. Phys. Chem. B. 119: 13807-13815.
Brecht, M., van Gastel, M., Buhrke, T., Friedrich, B., and Lubitz, W. (2003) Direct detection of a hydrogen ligand in the [NiFe] center of the regulatory H₂-sensing hydrogenase from Ralstonia eutropha in its reduced state by HYSCORE and ENDOR spectroscopy. J. Am. Chem. Soc. 125: 13073-13083.
Haumann, M., Porthun, A., Buhrke, T., Liebisch, P., Meyer-Klaucke, W., Friedrich, B., and Dau, H. (2003) Hydrogen-induced structural changes at the nickel site of the regulatory [NiFe] hydrogenase from Ralstonia eutropha detected by X-ray absorption spectroscopy. Biochem. 42: 11004-11015.
Löscher, S., Gebler, A., Stein, M., Sanganas, O., Buhrke, T., Zebger, I., Dau, H., Friedrich, B., Lenz, O., and Haumann, M. (2010) Protein-protein complex formation affects the Ni-Fe and Fe-S centers in the H₂-sensing regulatory hydrogenase from Ralstonia eutropha H16. Chemphyschem 11: 1297-1306.
Pierik, A.J., Schmelz, M., Lenz, O., Friedrich, B., and Albracht, S.P.J. (1998) Characterization of the active site of a hydrogen sensor from Alcaligenes eutrophus. FEBS J. 428: 231-235.
Roncaroli, F., Bill, E., Friedrich, B., Lenz, O., Lubitz, W., and Pandelia, M.E. (2015) Cofactor composition and function of a H₂-sensing regulatory hydrogenase as revealed by Mössbauer and EPR spectroscopy. Chem. Sci. 6: 4495-4507.