[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_028254735.1Veillonella magna[NiFe] Group 1dFirmicutesSelenomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_028257253.1Veillonella montpellierensis[NiFe] Group 1dFirmicutesSelenomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_004696380.1Veillonella parvula[NiFe] Group 1dFirmicutesSelenomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_006555093.1Veillonella ratti[NiFe] Group 1dFirmicutesSelenomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_019554568.1Zymophilus raffinosivorans[NiFe] Group 1dFirmicutesSelenomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_013764260.1Haliscomenobacter hydrossis[NiFe] Group 1dBacteroidetesSphingobacterialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_008510449.1Mucilaginibacter paludis[NiFe] Group 1dBacteroidetesSphingobacterialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_014217548.1Niastella koreensis[NiFe] Group 1dBacteroidetesSphingobacterialesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_008068262.1Novosphingobium nitrogenifigens[NiFe] Group 1dAlphaproteobacteriaSphingomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_002683184.1Beggiatoa alba[NiFe] Group 1dGammaproteobacteriaThiotrichalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_029908155.1Hydrogenovibrio marinus[NiFe] Group 1dGammaproteobacteriaThiotrichalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_029939087.1Thiomicrospira sp. MA2-6[NiFe] Group 1dGammaproteobacteriaThiotrichalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_020394857.1Thiothrix disciformis[NiFe] Group 1dGammaproteobacteriaThiotrichalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_002706872.1Thiothrix nivea[NiFe] Group 1dGammaproteobacteriaThiotrichalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_028007256.1Solimonas flava[NiFe] Group 1dGammaproteobacteriaXanthomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b
WP_020647929.1Solimonas variicoloris[NiFe] Group 1dGammaproteobacteriaXanthomonadalesAerobic UptakeTolerant3[NiFe]-centre, 1 x [4Fe3S] cluster, 1 x [3Fe4S] cluster, 1 x [4Fe4S] clusterCytochrome b

Literature

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