[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)
WP_011714112.1	Magnetococcus marinus	[NiFe] Group 2b	Alphaproteobacteria	Magnetococcales	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_012169127.1	Azorhizobium caulinodans	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_029004859.1	Azorhizobium doebereinerae	[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_029356684.1	Bosea sp. 117	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	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_028135604.1	Bradyrhizobium japonicum	[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_015597392.1	Hyphomicrobium denitrificans	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_026600034.1	Methylocystis sp. LW5	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	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_024878510.1	Methylosinus sp. LW3	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	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_003612204.1	Methylosinus trichosporium	[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_028738631.1	Rhizobium selenitireducens	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	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_011662668.1	Rhodopseudomonas palustris	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_022723662.1	Rhodopseudomonas sp. B29	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_028877931.1	Terasakiella pusilla	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	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_024281261.1	Xanthobacter sp. 126	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_029556474.1	Xanthobacter sp. 91	[NiFe] Group 2b	Alphaproteobacteria	Rhizobiales	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_008886444.1	Citreicella sp. SE45	[NiFe] Group 2b	Alphaproteobacteria	Rhodobacterales	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_024844879.1	Paracoccus pantotrophus	[NiFe] Group 2b	Alphaproteobacteria	Rhodobacterales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_028714014.1	Paracoccus sp. J55	[NiFe] Group 2b	Alphaproteobacteria	Rhodobacterales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_028717756.1	Paracoccus yeei	[NiFe] Group 2b	Alphaproteobacteria	Rhodobacterales	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_023918084.1	Rhodobacter capsulatus	[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_023664198.1	Rhodobacter sp. CACIA14H1	[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_002720656.1	Rhodobacter sphaeroides	[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_008282513.1	Roseovarius sp. TM1035	[NiFe] Group 2b	Alphaproteobacteria	Rhodobacterales	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_020043467.1	Salipiger mucosus	[NiFe] Group 2b	Alphaproteobacteria	Rhodobacterales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_025825893.1	Acetobacter okinawensis	[NiFe] Group 2b	Alphaproteobacteria	Rhodospiralles	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_029009282.1	Azospirillum halopraeferens	[NiFe] Group 2b	Alphaproteobacteria	Rhodospiralles	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_024080410.1	Magnetospirillum gryphiswaldense	[NiFe] Group 2b	Alphaproteobacteria	Rhodospiralles	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_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_008068222.1	Novosphingobium nitrogenifigens	[NiFe] Group 2b	Alphaproteobacteria	Sphingomonadales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
WP_026436955.1	Acidovorax sp. JHL-9	[NiFe] Group 2b	Betaproteobacteria	Burkholderiales	Sensory	Tolerant	4	[NiFe]-centre, 3 x [4Fe4S] clusters	Histidine kinase, response regulator
AAB49361.1	Alcaligenes hydrogenophilus	[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.