[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 |
|
| 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_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_011801344.1 | Polaromonas naphthalenivorans | [NiFe] Group 2b | Betaproteobacteria | Burkholderiales | Sensory | Tolerant | 4 | [NiFe]-centre, 3 x [4Fe4S] clusters | Histidine kinase, response regulator |
| WP_023105857.1 | Pseudomonas aeruginosa | [NiFe] Group 2b | Gammaproteobacteria | Pseudomonadales | 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_024762399.1 | Pseudomonas nitroreducens | [NiFe] Group 2b | Gammaproteobacteria | Pseudomonadales | 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_011153946.1 | Ralstonia eutropha | [NiFe] Group 2b | Betaproteobacteria | Burkholderiales | 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_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_011466381.1 | Rhodoferax ferrireducens | [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_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_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_014429792.1 | Rubrivivax gelatinosus | [NiFe] Group 2b | Betaproteobacteria | Burkholderiales | 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_028877931.1 | Terasakiella pusilla | [NiFe] Group 2b | Alphaproteobacteria | Rhizobiales | Sensory | Tolerant | 4 | [NiFe]-centre, 3 x [4Fe4S] clusters | Histidine kinase, response regulator |
| WP_019642787.1 | Thioalkalivibrio sp. ALSr1 | [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 |
| AAX40740.1 | Thiocapsa roseopersicina | [NiFe] Group 2b | Gammaproteobacteria | Chromatiales | 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_007041639.1 | Thiorhodococcus drewsii | [NiFe] Group 2b | Gammaproteobacteria | Chromatiales | Sensory | Tolerant | 4 | [NiFe]-centre, 3 x [4Fe4S] clusters | Histidine kinase, response regulator |
| WP_020394871.1 | Thiothrix disciformis | [NiFe] Group 2b | Gammaproteobacteria | Thiotrichales | 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_018904285.1 | Variovorax paradoxus | [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_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 |
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.