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Cryo-EM structure of the F420-reducing NiFe-hydrogenase from a methanogenic archaeon with bound substrate

Source organism: Methanothermobacter marburgensis
Biochemical function: iron-sulfur cluster binding
Biological process: not assigned
Cellular component: not assigned

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EC 1.12.98.1: Coenzyme F420 hydrogenase

Reaction catalysed:
H(2) + oxidized coenzyme F420 = reduced coenzyme F420
Systematic name:
Hydrogen:coenzyme F420 oxidoreductase
Alternative Name(s):
  • 8-hydroxy-5-deazaflavin-reducing hydrogenase
  • Coenzyme F420-dependent hydrogenase
  • F420-reducing hydrogenase

GO terms

Sequence families

Pfam Protein families (Pfam)
PF00374
Domain description: Nickel-dependent hydrogenase
Occurring in:
  1. F420-reducing hydrogenase, subunit alpha
The deposited structure of PDB entry 3zfs contains 2 copies of Pfam domain PF00374 (Nickel-dependent hydrogenase) in F420-reducing hydrogenase, subunit alpha. Showing 2 copies in chain A.

PF04432
Domain description: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
Occurring in:
  1. F420-reducing hydrogenase, subunit beta
The deposited structure of PDB entry 3zfs contains 1 copy of Pfam domain PF04432 (Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus) in F420-reducing hydrogenase, subunit beta. Showing 1 copy in chain C.

PF04422
Domain description: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term
Occurring in:
  1. F420-reducing hydrogenase, subunit beta
The deposited structure of PDB entry 3zfs contains 1 copy of Pfam domain PF04422 (Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term) in F420-reducing hydrogenase, subunit beta. Showing 1 copy in chain C.

PF13187
Domain description: 4Fe-4S dicluster domain
Occurring in:
  1. 4Fe-4S ferredoxin-type domain-containing protein

PF01058
Domain description: NADH ubiquinone oxidoreductase, 20 Kd subunit
Occurring in:
  1. 4Fe-4S ferredoxin-type domain-containing protein
The deposited structure of PDB entry 3zfs contains 1 copy of Pfam domain PF01058 (NADH ubiquinone oxidoreductase, 20 Kd subunit) in 4Fe-4S ferredoxin-type domain-containing protein. Showing 1 copy in chain B.

InterPro InterPro annotations
IPR017896
Domain description: 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Occurring in:
  1. 4Fe-4S ferredoxin-type domain-containing protein
IPR018194
Domain description: Nickel-dependent hydrogenase, large subunit, nickel binding site
Occurring in:
  1. F420-reducing hydrogenase, subunit alpha
IPR001501
Domain description: Nickel-dependent hydrogenase, large subunit
Occurring in:
  1. F420-reducing hydrogenase, subunit alpha
IPR029014
Domain description: [NiFe]-hydrogenase, large subunit
Occurring in:
  1. F420-reducing hydrogenase, subunit alpha
IPR007525
Domain description: Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal
Occurring in:
  1. F420-reducing hydrogenase, subunit beta
IPR007516
Domain description: Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal
Occurring in:
  1. F420-reducing hydrogenase, subunit beta
IPR017679
Domain description: Coenzyme F420 hydrogenase subunit beta, archaea
Occurring in:
  1. F420-reducing hydrogenase, subunit beta
IPR045220
Domain description: Oxidoreductase FRHB/FDHB/HCAR-like
Occurring in:
  1. F420-reducing hydrogenase, subunit beta
IPR017900
Domain description: 4Fe-4S ferredoxin, iron-sulphur binding, conserved site
Occurring in:
  1. 4Fe-4S ferredoxin-type domain-containing protein
IPR006137
Domain description: NADH:ubiquinone oxidoreductase-like, 20kDa subunit
Occurring in:
  1. 4Fe-4S ferredoxin-type domain-containing protein
IPR017681
Domain description: Coenzyme F420 hydrogenase, subunit gamma
Occurring in:
  1. 4Fe-4S ferredoxin-type domain-containing protein
IPR037024
Domain description: [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily
Occurring in:
  1. 4Fe-4S ferredoxin-type domain-containing protein
IPR017682
Domain description: Coenzyme F420 hydrogenase, subunit alpha
Occurring in:
  1. F420-reducing hydrogenase, subunit alpha

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