[NiFe] Group 1d-hydrogenase

This entry was last updated at: Feb. 9, 2018, 7:26 a.m.

Properties
Group [NiFe] Group 1: Respiratory H2-uptake [NiFe] hydrogenases
Subgroup [NiFe] Group 1d: Oxygen-tolerant
Function Hydrogenotrophic respiration using O2 or fumarate as terminal electron acceptors. Enzyme transfers H2-liberated electrons through cyt b and quinone to terminal reductase.
Activity H2-uptake (unidirectional)
Oxygen tolerance O2-tolerant
Localisation Membrane-bound
Distribution
Ecosystem distribution Diverse soil, aquatic, and host-associated environments
Taxonomic distribution Widespread among obligately aerobic and facultatively anaerobic bacteria
Genetic Organisation

e.g. Escherichia coli (WP_021522685.1):

Architecture
Structures
  • 3AYX (Hydrogenovibrio marinus, 1.2 Å resolution, active)
  • 3AYZ (Hydrogenovibrio marinus, 1.3 Å resolution, oxidized)
  • 3AYY (Hydrogenovibrio marinus, 1.3 Å resolution, superoxidized)
  • 3RGW (Ralstonia eutropha, 1.5 Å resolution, active)
  • 4IUD (Ralstonia eutropha, 1.5 Å resolution, reduced)
  • 4IUB (Ralstonia eutropha, 1.6 Å resolution, oxidised)
  • 4IUC (Ralstonia eutropha, 1.5 Å resolution, superoxidised)
  • 5ADU (Escherichia coli, 1.1 Å resolution, oxidised)
  • 3UQY (Escherichia coli, 1.5 Å resolution, active)
  • 3USE (Escherichia coli, 1.7 Å resolution, oxidised)
  • 5A4M (Escherichia coli, 1.7 Å resolution, oxidised)
  • 3USC (Escherichia coli, 2.0 Å resolution, superoxidised)
  • 4GD3 (Escherichia coli, 3.3 Å resolution, with cyt b)
  • 4C3O (Salmonella enterica, 3.2 Å resolution, oxidised)
Subunits 3
Subunit description HyaB (hydrogenase large subunit)
HyaA (hydrogenase small subunit)
HyaC (cytochrome b subunit)
Catalytic site [NiFe]-centre
FeS clusters Proximal: 6Cys[4Fe3S]
Medial: 3Cys[3Fe4S]
Distal: 3Cys1His[4Fe4S]
Sequences in this class
NCBI AccessionOrganismHydrogenase ClassPhylumOrderActivity (Predicted)Oxygen Tolerance (Predicted)Subunits (Predicted)Metal Centres (Predicted)Accessory Subunits (Predicted)
WP_009059758.1Methylacidiphilum fumariolicum[NiFe] Group 1dVerrucomicrobiaMethylacidiphilalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_012463656.1Methylacidiphilum infernorum[NiFe] Group 1dVerrucomicrobiaMethylacidiphilalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_027157817.1Methylobacter luteus[NiFe] Group 1dGammaproteobacteriaMethylococcalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_020157432.1Methylobacter marinus[NiFe] Group 1dGammaproteobacteriaMethylococcalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_027149878.1Methylobacter tundripaludum[NiFe] Group 1dGammaproteobacteriaMethylococcalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_026610556.1Methylocaldum szegediense[NiFe] Group 1dGammaproteobacteriaMethylococcalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_017366017.1Methylococcus capsulatus[NiFe] Group 1dGammaproteobacteriaMethylococcalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_013818449.1Methylomonas methanica[NiFe] Group 1dGammaproteobacteriaMethylococcalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_026603256.1Methylomonas sp. 11b[NiFe] Group 1dGammaproteobacteriaMethylococcalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_020483431.1Methylomonas sp. MK1[NiFe] Group 1dGammaproteobacteriaMethylococcalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_019865813.1Methylovulum miyakonense[NiFe] Group 1dGammaproteobacteriaMethylococcalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
CUU03002.1Kryptonium thompsoni[NiFe] Group 1dKryptoniaN/AAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_014450582.1Leptospirillum ferrooxidans[NiFe] Group 1dNitrospiraeNitrospiralesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_007019929.1Neptuniibacter caesariensis[NiFe] Group 1dGammaproteobacteriaOceanospirillalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_028293254.1Oceanobacter kriegii[NiFe] Group 1dGammaproteobacteriaOceanospirillalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_028302021.1Oceanospirillum beijerinckii[NiFe] Group 1dGammaproteobacteriaOceanospirillalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_012703499.1 Azotobacter vinelandii[NiFe] Group 1dGammaproteobacteriaPseudomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_023105852.1Pseudomonas aeruginosa[NiFe] Group 1dGammaproteobacteriaPseudomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_010563027.1Pseudomonas extremaustralis[NiFe] Group 1dGammaproteobacteriaPseudomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_024762404.1Pseudomonas nitroreducens[NiFe] Group 1dGammaproteobacteriaPseudomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_017845591.1Pseudomonas veronii[NiFe] Group 1dGammaproteobacteriaPseudomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_018391449.1 Ancylobacter sp. FA202[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_012169130.1Azorhizobium caulinodans[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_029004862.1Azorhizobium doebereinerae[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_012384150.1Beijerinckia indica[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_029356678.1Bosea sp. 117[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_028336746.1Bradyrhizobium elkanii[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_028135606.1Bradyrhizobium japonicum[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_015668917.1Bradyrhizobium oligotrophicum[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_018240255.1Ensifer sp. BR816[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_008838370.1Mesorhizobium alhagi[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_006205723.1Mesorhizobium amorphae[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_016919626.1Methylocystis parvus[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_026600032.1Methylocystis sp. LW5[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_014891816.1Methylocystis sp. SC2[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_024878508.1Methylosinus sp. LW3[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_018266919.1Methylosinus sp. LW4[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_003612200.1Methylosinus trichosporium[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_013913761.1Oligotropha carboxidovorans[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_026783388.1Pleomorphomonas koreensis[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_026790280.1Pleomorphomonas oryzae[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_018517046.1Rhizobium leguminosarum[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_022718972.1Rhizobium mongolense[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_028738633.1Rhizobium selenitireducens[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_023664202.1Rhodobacter sp. CACIA14H1[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_013418645.1Rhodomicrobium vannielii[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_011156496.1Rhodopseudomonas palustris[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_022723664.1Rhodopseudomonas sp. B29[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_028002579.1Sinorhizobium arboris[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_018098934.1Sinorhizobium meliloti[NiFe] Group 1dAlphaproteobacteriaRhizobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b

Literature

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