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Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Thermoanaerobacter kivui in the oxidised state

Source organism: Thermoanaerobacter kivui
Biochemical function: hydrogen dehydrogenase (NADP+) activity
Biological process: proton transmembrane transport
Cellular component: membrane

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EC 1.12.1.3: Hydrogen dehydrogenase (NADP(+))

Reaction catalysed:
H(2) + NADP(+) = H(+) + NADPH
Systematic name:
Hydrogen:NADP(+) oxidoreductase
Alternative Name(s):
  • Hydrogenase
  • Hydrogenase I
  • NADP(+)-linked hydrogenase
  • NADP(+)-reducing hydrogenase

GO terms

Sequence families

Pfam Protein families (Pfam)
PF01257
Domain description: Thioredoxin-like [2Fe-2S] ferredoxin
Occurring in:
  1. 4Fe-4S ferredoxin-type domain-containing protein
  2. Electron bifurcating hydrogenase subunit HydC
The deposited structure of PDB entry 8bew contains 2 copies of Pfam domain PF01257 (Thioredoxin-like [2Fe-2S] ferredoxin) in 4Fe-4S ferredoxin-type domain-containing protein. Showing 1 copy in chain B.
The deposited structure of PDB entry 8bew contains 2 copies of Pfam domain PF01257 (Thioredoxin-like [2Fe-2S] ferredoxin) in Electron bifurcating hydrogenase subunit HydC. Showing 1 copy in chain C.

PF12838
Domain description: 4Fe-4S dicluster domain
Occurring in:
  1. 4Fe-4S ferredoxin-type domain-containing protein
The deposited structure of PDB entry 8bew contains 2 copies of Pfam domain PF12838 (4Fe-4S dicluster domain) in 4Fe-4S ferredoxin-type domain-containing protein. Showing 1 copy in chain B.

PF10589
Domain description: NADH-ubiquinone oxidoreductase-F iron-sulfur binding region
Occurring in:
  1. 4Fe-4S ferredoxin-type domain-containing protein
The deposited structure of PDB entry 8bew contains 2 copies of Pfam domain PF10589 (NADH-ubiquinone oxidoreductase-F iron-sulfur binding region) in 4Fe-4S ferredoxin-type domain-containing protein. Showing 1 copy in chain B.

PF01512
Domain description: Respiratory-chain NADH dehydrogenase 51 Kd subunit
Occurring in:
  1. 4Fe-4S ferredoxin-type domain-containing protein
The deposited structure of PDB entry 8bew contains 2 copies of Pfam domain PF01512 (Respiratory-chain NADH dehydrogenase 51 Kd subunit) in 4Fe-4S ferredoxin-type domain-containing protein. Showing 1 copy in chain B.

PF02256
Domain description: Iron hydrogenase small subunit
Occurring in:
  1. Electron bifurcating hydrogenase subunit HydA1
The deposited structure of PDB entry 8bew contains 2 copies of Pfam domain PF02256 (Iron hydrogenase small subunit) in Electron bifurcating hydrogenase subunit HydA1. Showing 1 copy in chain A.

PF02906
Domain description: Iron only hydrogenase large subunit, C-terminal domain
Occurring in:
  1. Electron bifurcating hydrogenase subunit HydA1
The deposited structure of PDB entry 8bew contains 2 copies of Pfam domain PF02906 (Iron only hydrogenase large subunit, C-terminal domain) in Electron bifurcating hydrogenase subunit HydA1. Showing 1 copy in chain A.

PF22117
Domain description: NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain
Occurring in:
  1. Electron bifurcating hydrogenase subunit HydA1

PF10588
Domain description: NADH-ubiquinone oxidoreductase-G iron-sulfur binding region
Occurring in:
  1. Electron bifurcating hydrogenase subunit HydA1
The deposited structure of PDB entry 8bew contains 2 copies of Pfam domain PF10588 (NADH-ubiquinone oxidoreductase-G iron-sulfur binding region) in Electron bifurcating hydrogenase subunit HydA1. Showing 1 copy in chain A.

PF13510
Domain description: 2Fe-2S iron-sulfur cluster binding domain
Occurring in:
  1. Electron bifurcating hydrogenase subunit HydA1
The deposited structure of PDB entry 8bew contains 2 copies of Pfam domain PF13510 (2Fe-2S iron-sulfur cluster binding domain) in Electron bifurcating hydrogenase subunit HydA1. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR017896
Domain description: 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Occurring in:
  1. Electron bifurcating hydrogenase subunit HydA1
  2. 4Fe-4S ferredoxin-type domain-containing protein
IPR017900
Domain description: 4Fe-4S ferredoxin, iron-sulphur binding, conserved site
Occurring in:
  1. Electron bifurcating hydrogenase subunit HydA1
  2. 4Fe-4S ferredoxin-type domain-containing protein
IPR002023
Domain description: NADH-quinone oxidoreductase subunit E-like
Occurring in:
  1. Electron bifurcating hydrogenase subunit HydC
IPR019574
Domain description: NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding
Occurring in:
  1. Electron bifurcating hydrogenase subunit HydA1
IPR019575
Domain description: NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain
Occurring in:
  1. 4Fe-4S ferredoxin-type domain-containing protein
IPR037207
Domain description: NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily
Occurring in:
  1. 4Fe-4S ferredoxin-type domain-containing protein
IPR037225
Domain description: NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily
Occurring in:
  1. 4Fe-4S ferredoxin-type domain-containing protein
IPR036249
Domain description: Thioredoxin-like superfamily
Occurring in:
  1. 4Fe-4S ferredoxin-type domain-containing protein
  2. Electron bifurcating hydrogenase subunit HydC
IPR003149
Domain description: Iron hydrogenase, small subunit
Occurring in:
  1. Electron bifurcating hydrogenase subunit HydA1
IPR001041
Domain description: 2Fe-2S ferredoxin-type iron-sulfur binding domain
Occurring in:
  1. Electron bifurcating hydrogenase subunit HydA1
IPR042128
Domain description: NuoE domain
Occurring in:
  1. Electron bifurcating hydrogenase subunit HydC
IPR041921
Domain description: NADH-quinone oxidoreductase subunit E, N-terminal
Occurring in:
  1. Electron bifurcating hydrogenase subunit HydC
IPR028431
Domain description: NADP-reducing hydrogenase subunit HndA-like
Occurring in:
  1. Electron bifurcating hydrogenase subunit HydC
IPR001949
Domain description: NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site
Occurring in:
  1. 4Fe-4S ferredoxin-type domain-containing protein
IPR019554
Domain description: Soluble ligand binding domain
Occurring in:
  1. 4Fe-4S ferredoxin-type domain-containing protein
IPR011538
Domain description: NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain
Occurring in:
  1. 4Fe-4S ferredoxin-type domain-containing protein
IPR036991
Domain description: Iron hydrogenase, small subunit superfamily
Occurring in:
  1. Electron bifurcating hydrogenase subunit HydA1
IPR004108
Domain description: Iron hydrogenase, large subunit, C-terminal
Occurring in:
  1. Electron bifurcating hydrogenase subunit HydA1
IPR009016
Domain description: Iron hydrogenase
Occurring in:
  1. Electron bifurcating hydrogenase subunit HydA1
IPR013352
Domain description: Iron hydrogenase, subset
Occurring in:
  1. Electron bifurcating hydrogenase subunit HydA1
IPR000283
Domain description: NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site
Occurring in:
  1. Electron bifurcating hydrogenase subunit HydA1
IPR036010
Domain description: 2Fe-2S ferredoxin-like superfamily
Occurring in:
  1. Electron bifurcating hydrogenase subunit HydA1

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