Function and Biology

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

Source organism: Methanothermobacter marburgensis
Biochemical function: nickel cation binding
Biological process: oxidation-reduction process
Cellular component: not assigned

EC 1.12.98.1: Coenzyme F420 hydrogenase

Reaction catalysed:
H(2) + oxidized coenzyme F420 = reduced coenzyme F420.
Comments:
  • The enzyme from some sources contains selenocysteine.
  • The enzyme also reduces the riboflavin analog of F420, flavins and methylviologen, but to a lesser extent.
  • The hydrogen acceptor coenzyme F420 is a deazaflavin derivative.
  • Formerly EC 1.12.99.1.
Systematic name:
Hydrogen:coenzyme F420 oxidoreductase
Alternative Name(s):
  • 8-hydroxy-5-deazaflavin-reducing hydrogenase
  • F420-reducing hydrogenase
  • Coenzyme F420-dependent hydrogenase

Sequence families

CATH Protein families (Pfam)
PF00037
Domain description: 4Fe-4S binding domain
Occurring in:
  1. F420-reducing hydrogenase, subunit gamma
2 copies of Pfam domain PF00037 (4Fe-4S binding domain) in F420-reducing hydrogenase, subunit gamma in PDB 3zfs.

PF00374
Domain description: Nickel-dependent hydrogenase
Occurring in:
  1. F420-reducing hydrogenase, subunit alpha
2 copies of Pfam domain PF00374 (Nickel-dependent hydrogenase) in F420-reducing hydrogenase, subunit alpha in PDB 3zfs.

PF04422
Domain description: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term
Occurring in:
  1. F420-reducing hydrogenase, subunit beta
1 copy of Pfam domain PF04422 (Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term) in F420-reducing hydrogenase, subunit beta in PDB 3zfs.

PF01058
Domain description: NADH ubiquinone oxidoreductase, 20 Kd subunit
Occurring in:
  1. F420-reducing hydrogenase, subunit gamma
1 copy of Pfam domain PF01058 (NADH ubiquinone oxidoreductase, 20 Kd subunit) in F420-reducing hydrogenase, subunit gamma in PDB 3zfs.

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

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