[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_006366944.1Chlorobium ferrooxidans[NiFe] Group 1dChlorobiChlorobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_012465814.1Chlorobium limicola[NiFe] Group 1dChlorobiChlorobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_011744848.1Chlorobium phaeobacteroides[NiFe] Group 1dChlorobiChlorobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_012501193.1Chloroherpeton thalassium[NiFe] Group 1dChlorobiChlorobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_011358178.1Pelodictyon luteolum[NiFe] Group 1dChlorobiChlorobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_012508571.1Pelodictyon phaeoclathratiforme[NiFe] Group 1dChlorobiChlorobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_012505437.1Prosthecochloris aestuarii[NiFe] Group 1dChlorobiChlorobialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_009378513.1Bilophila sp. 4_1_30[NiFe] Group 1dDeltaproteobacteriaDesulfovibrionalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_005026843.1Bilophila wadsworthia[NiFe] Group 1dDeltaproteobacteriaDesulfovibrionalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_011526524.1Lawsonia intracellularis[NiFe] Group 1dDeltaproteobacteriaDesulfovibrionalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_027414715.1Aneurinibacillus terranovensis[NiFe] Group 1dFirmicutesBacillalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_003397243.1Anoxybacillus flavithermus[NiFe] Group 1dFirmicutesBacillalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_019416530.1Anoxybacillus kamchatkensis[NiFe] Group 1dFirmicutesBacillalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_009361199.1Anoxybacillus sp. DT3-1[NiFe] Group 1dFirmicutesBacillalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_021094790.1Anoxybacillus sp. SK3-4[NiFe] Group 1dFirmicutesBacillalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_003330153.1Bacillus azotoformans[NiFe] Group 1dFirmicutesBacillalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_019241710.1Bacillus massilioanorexius[NiFe] Group 1dFirmicutesBacillalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_020062534.1Bacillus sp. 123MFChir2[NiFe] Group 1dFirmicutesBacillalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_015594636.1Bacillus sp. 1NLA3E[NiFe] Group 1dFirmicutesBacillalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_013400922.1Geobacillus sp. Y4.1MC1[NiFe] Group 1dFirmicutesBacillalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_013876989.1Geobacillus thermoglucosidasius[NiFe] Group 1dFirmicutesBacillalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_028552966.1Paenibacillus sp. UNC451MF[NiFe] Group 1dFirmicutesBacillalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_023510524.1Sporolactobacillus laevolacticus[NiFe] Group 1dFirmicutesBacillalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_010631937.1Sporolactobacillus vineae[NiFe] Group 1dFirmicutesBacillalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_025206080.1Dehalobacter restrictus[NiFe] Group 1dFirmicutesClostridialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_019226053.1Dehalobacter sp. E1[NiFe] Group 1dFirmicutesClostridialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_026156348.1Dehalobacter sp. FTH1[NiFe] Group 1dFirmicutesClostridialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_014794600.1Desulfitobacterium dehalogenans[NiFe] Group 1dFirmicutesClostridialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_015261076.1Desulfitobacterium dichloroeliminans[NiFe] Group 1dFirmicutesClostridialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_005811167.1Desulfitobacterium hafniense[NiFe] Group 1dFirmicutesClostridialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_019850866.1Desulfitobacterium sp. PCE1[NiFe] Group 1dFirmicutesClostridialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_014826810.1Desulfosporosinus acidiphilus[NiFe] Group 1dFirmicutesClostridialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_014904046.1Desulfosporosinus meridiei[NiFe] Group 1dFirmicutesClostridialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_014186363.1Desulfosporosinus orientis[NiFe] Group 1dFirmicutesClostridialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_009623566.1Desulfosporosinus sp. OT[NiFe] Group 1dFirmicutesClostridialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_012281726.1Heliobacterium modesticaldum[NiFe] Group 1dFirmicutesClostridialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_012282567.1Heliobacterium modesticaldum[NiFe] Group 1dFirmicutesClostridialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_004573252.1Acetonema longum[NiFe] Group 1dFirmicutesSelenomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_027937761.1Anaeroarcus burkinensis[NiFe] Group 1dFirmicutesSelenomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_018702099.1Anaeromusa acidaminophila[NiFe] Group 1dFirmicutesSelenomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_006305436.1Centipeda periodontii[NiFe] Group 1dFirmicutesSelenomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_015597373.1Hyphomicrobium denitrificans[NiFe] Group 1dFirmicutesSelenomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_027889016.1Megamonas hypermegale[NiFe] Group 1dFirmicutesSelenomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_005840788.1Mitsuokella multacida[NiFe] Group 1dFirmicutesSelenomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_007954318.1Pelosinus fermentans[NiFe] Group 1dFirmicutesSelenomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_026762838.1Selenomonas artemidis[NiFe] Group 1dFirmicutesSelenomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_019542170.1Selenomonas bovis[NiFe] Group 1dFirmicutesSelenomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_006690835.1Selenomonas flueggei[NiFe] Group 1dFirmicutesSelenomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_006692428.1Selenomonas infelix[NiFe] Group 1dFirmicutesSelenomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_006696448.1Selenomonas noxia[NiFe] Group 1dFirmicutesSelenomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b

Literature

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