[NiFe] Group 2c-hydrogenase Putative
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 2c: Diguanylate cyclase-linked |
| Function | Undetermined role. May serve as H2-sensors in regulatory cascades. Enzyme predicted to transfer H2-liberated electrons to PAS domain. Associated redox change may modulate cyclic di-GMP production and in turn various cellular processes. |
| Activity | H2-sensing? |
| Oxygen tolerance | O2-tolerant? |
| Localisation | Cytosolic? |
Distribution
| Ecosystem distribution | In low abundance in various soil and aquatic samples |
| Taxonomic distribution | Exclusive to Proteobacteria, including methanotrophic Gammaproteobacteria and sulfate-reducing Deltaproteobacteria |
Genetic Organisation
e.g. Magnetospirillum magneticum (WP_011383527.1):
Architecture
| Structures |
|
| Subunits | 3? |
| Subunit description | HurL (hydrogenase large subunit) HurS (hydrogenase small subunit) HurR (putative diguanylate cyclase and phosphodiesterase) |
| Catalytic site | [NiFe]-centre |
| FeS clusters | Proximal: 3Cys1Asp[4Fe4S] or 3Cys1Glu[4Fe4S] Medial: 3Cys[3Fe4S] Distal: 3Cys1His[4Fe4S] |
Important Notes
This hydrogenase class has only been identified based on genomic predictions. The genetic organisation of the operon encoding this enzyme strongly suggests a role in cyclic di-GMP production, but this needs to be validated through physiological, biochemical, and genetic studies.
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_011288617.1 | Dechloromonas aromatica | [NiFe] Group 2c | Betaproteobacteria | Rhodocyclales | Sensory | Tolerant | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Diguanylate cyclase / phosphodiesterase |
| WP_028315676.1 | Desulfatibacillum aliphaticivorans | [NiFe] Group 2c | Deltaproteobacteria | Desulfobacterales | Sensory | Tolerant | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Diguanylate cyclase / phosphodiesterase |
| WP_015947049.1 | Desulfatibacillum alkenivorans | [NiFe] Group 2c | Deltaproteobacteria | Desulfobacterales | Sensory | Tolerant | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Diguanylate cyclase / phosphodiesterase |
| WP_028584585.1 | Desulfobulbus mediterraneus | [NiFe] Group 2c | Deltaproteobacteria | Desulfobacterales | Sensory | Tolerant | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Diguanylate cyclase / phosphodiesterase |
| WP_015724478.1 | Desulfobulbus propionicus | [NiFe] Group 2c | Deltaproteobacteria | Desulfobacterales | Sensory | Tolerant | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Diguanylate cyclase / phosphodiesterase |
| WP_008870999.1 | Desulfonatronospira thiodismutans | [NiFe] Group 2c | Deltaproteobacteria | Desulfovibrionales | Sensory | Tolerant | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Diguanylate cyclase / phosphodiesterase |
| WP_024334199.1 | Desulfotignum balticum | [NiFe] Group 2c | Deltaproteobacteria | Desulfobacterales | Sensory | Tolerant | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Diguanylate cyclase / phosphodiesterase |
| WP_006965253.1 | Desulfotignum phosphitoxidans | [NiFe] Group 2c | Deltaproteobacteria | Desulfobacterales | Sensory | Tolerant | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Diguanylate cyclase / phosphodiesterase |
| WP_005505415.1 | Grimontia hollisae | [NiFe] Group 2c | Gammaproteobacteria | Vibrionales | Sensory | Tolerant | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Diguanylate cyclase / phosphodiesterase |
| WP_022980127.1 | Ideonella sp. B508-1 | [NiFe] Group 2c | Betaproteobacteria | Burkholderiales | Sensory | Tolerant | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Diguanylate cyclase / phosphodiesterase |
| WP_012346378.1 | Leptothrix cholodnii | [NiFe] Group 2c | Betaproteobacteria | Burkholderiales | Sensory | Tolerant | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Diguanylate cyclase / phosphodiesterase |
| WP_011383527.1 | Magnetospirillum magneticum | [NiFe] Group 2c | Alphaproteobacteria | Rhodospiralles | Sensory | Tolerant | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Diguanylate cyclase / phosphodiesterase |
| WP_027150633.1 | Methylobacter tundripaludum | [NiFe] Group 2c | Gammaproteobacteria | Methylococcales | Sensory | Tolerant | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Diguanylate cyclase / phosphodiesterase |
| WP_005373434.1 | Methylomicrobium album | [NiFe] Group 2c | Gammaproteobacteria | Methylococcales | Sensory | Tolerant | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Diguanylate cyclase / phosphodiesterase |
| WP_014150136.1 | Methylomicrobium alcaliphilum | [NiFe] Group 2c | Gammaproteobacteria | Methylococcales | Sensory | Tolerant | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Diguanylate cyclase / phosphodiesterase |
| WP_017841795.1 | Methylomicrobium buryatense | [NiFe] Group 2c | Gammaproteobacteria | Methylococcales | Sensory | Tolerant | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Diguanylate cyclase / phosphodiesterase |
| WP_013818241.1 | Methylomonas methanica | [NiFe] Group 2c | Gammaproteobacteria | Methylococcales | Sensory | Tolerant | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Diguanylate cyclase / phosphodiesterase |
| WP_019867142.1 | Methylovulum miyakonense | [NiFe] Group 2c | Gammaproteobacteria | Methylococcales | Sensory | Tolerant | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Diguanylate cyclase / phosphodiesterase |
| WP_007019558.1 | Neptuniibacter caesariensis | [NiFe] Group 2c | Gammaproteobacteria | Oceanospirillales | Sensory | Tolerant | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Diguanylate cyclase / phosphodiesterase |
| WP_007041459.1 | Thiorhodococcus drewsii | [NiFe] Group 2c | Gammaproteobacteria | Chromatiales | Sensory | Tolerant | 3 | [NiFe]-centre, 2 x [4Fe4S] clusters, 1 x [3Fe4S] cluster | Diguanylate cyclase / phosphodiesterase |
Literature
Genetics:
- Greening, C., Biswas, A., Carere, C.R., Jackson, C.J., Taylor, M.C., Stott, M.B., Cook, G.M., and 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.