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1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS

Source organism: Nitratidesulfovibrio vulgaris str. Hildenborough
Biochemical function: iron-sulfur cluster binding
Biological process: not assigned
Cellular component: periplasmic space

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EC 1.12.7.2: Ferredoxin hydrogenase

Reaction catalysed:
H(2) + 2 oxidized ferredoxin = 2 reduced ferredoxin + 2 H(+)
Systematic name:
Hydrogen:ferredoxin oxidoreductase
Alternative Name(s):
  • Bidirectional hydrogenase
  • H(2) oxidizing hydrogenase
  • H(2) producing hydrogenase
  • Hydrogen-lyase
  • Hydrogenase
  • Hydrogenase (ferredoxin)
  • Hydrogenase I
  • Hydrogenase II
  • Hydrogenlyase
  • Uptake hydrogenase

GO terms

Biochemical function:
Biological process:
  • not assigned
Cellular component:

Sequence families

Pfam Protein families (Pfam)
PF00037
Domain description: 4Fe-4S binding domain
Occurring in:
  1. Periplasmic [Fe] hydrogenase large subunit
The deposited structure of PDB entry 1hfe contains 4 copies of Pfam domain PF00037 (4Fe-4S binding domain) in Periplasmic [Fe] hydrogenase large subunit. Showing 2 copies in chain B [auth L].

PF02256
Domain description: Iron hydrogenase small subunit
Occurring in:
  1. Periplasmic [Fe] hydrogenase small subunit
The deposited structure of PDB entry 1hfe contains 2 copies of Pfam domain PF02256 (Iron hydrogenase small subunit) in Periplasmic [Fe] hydrogenase small subunit. Showing 1 copy in chain A [auth S].

PF02906
Domain description: Iron only hydrogenase large subunit, C-terminal domain
Occurring in:
  1. Periplasmic [Fe] hydrogenase large subunit
The deposited structure of PDB entry 1hfe contains 2 copies of Pfam domain PF02906 (Iron only hydrogenase large subunit, C-terminal domain) in Periplasmic [Fe] hydrogenase large subunit. Showing 1 copy in chain B [auth L].

InterPro InterPro annotations
IPR017896
Domain description: 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Occurring in:
  1. Periplasmic [Fe] hydrogenase large subunit
IPR003149
Domain description: Iron hydrogenase, small subunit
Occurring in:
  1. Periplasmic [Fe] hydrogenase small subunit
IPR017900
Domain description: 4Fe-4S ferredoxin, iron-sulphur binding, conserved site
Occurring in:
  1. Periplasmic [Fe] hydrogenase large subunit
IPR008953
Domain description: Iron hydrogenase, small subunit HydB-type
Occurring in:
  1. Periplasmic [Fe] hydrogenase small subunit
IPR036991
Domain description: Iron hydrogenase, small subunit superfamily
Occurring in:
  1. Periplasmic [Fe] hydrogenase small subunit
IPR019546
Domain description: Twin-arginine translocation pathway, signal sequence, bacterial/archaeal
Occurring in:
  1. Periplasmic [Fe] hydrogenase small subunit
IPR006311
Domain description: Twin-arginine translocation pathway, signal sequence
Occurring in:
  1. Periplasmic [Fe] hydrogenase small subunit
IPR004108
Domain description: Iron hydrogenase, large subunit, C-terminal
Occurring in:
  1. Periplasmic [Fe] hydrogenase large subunit
IPR009016
Domain description: Iron hydrogenase
Occurring in:
  1. Periplasmic [Fe] hydrogenase large subunit
IPR013352
Domain description: Iron hydrogenase, subset
Occurring in:
  1. Periplasmic [Fe] hydrogenase large subunit

Structure domains

CATH CATH domains
3.40.50.1780
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Rossmann fold
Homology: Rossmann fold
Occurring in:
  1. Periplasmic [Fe] hydrogenase large subunit
The deposited structure of PDB entry 1hfe contains 2 copies of CATH domain 3.40.50.1780 (Rossmann fold) in Periplasmic [Fe] hydrogenase large subunit. Showing 1 copy in chain B [auth L].
3.40.950.10
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3
Homology: Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3
Occurring in:
  1. Periplasmic [Fe] hydrogenase large subunit
The deposited structure of PDB entry 1hfe contains 2 copies of CATH domain 3.40.950.10 (Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3) in Periplasmic [Fe] hydrogenase large subunit. Showing 1 copy in chain B [auth L].
4.10.260.20
Class: Few Secondary Structures
Architecture: Irregular
Topology: G Protein Gi Gamma 2
Homology: Iron hydrogenase, small subunit
Occurring in:
  1. Periplasmic [Fe] hydrogenase small subunit
The deposited structure of PDB entry 1hfe contains 2 copies of CATH domain 4.10.260.20 (G Protein Gi Gamma 2) in Periplasmic [Fe] hydrogenase small subunit. Showing 1 copy in chain A [auth S].
3.30.70.20
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Alpha-Beta Plaits
Homology: Alpha-Beta Plaits
Occurring in:
  1. Periplasmic [Fe] hydrogenase large subunit
The deposited structure of PDB entry 1hfe contains 2 copies of CATH domain 3.30.70.20 (Alpha-Beta Plaits) in Periplasmic [Fe] hydrogenase large subunit. Showing 1 copy in chain B [auth L].
SCOP SCOP annotations
48675
Class: All alpha proteins
Fold: Non-globular all-alpha subunits of globular proteins
Superfamily: Fe-only hydrogenase smaller subunit
Occurring in:
  1. Periplasmic [Fe] hydrogenase small subunit
The deposited structure of PDB entry 1hfe contains 2 copies of SCOP domain 48675 (Fe-only hydrogenase smaller subunit) in Periplasmic [Fe] hydrogenase small subunit. Showing 1 copy in chain A [auth S].
53921
Class: Alpha and beta proteins (a/b)
Fold: Fe-only hydrogenase
Superfamily: Fe-only hydrogenase
Occurring in:
  1. Periplasmic [Fe] hydrogenase large subunit
The deposited structure of PDB entry 1hfe contains 2 copies of SCOP domain 53921 (Fe-only hydrogenase) in Periplasmic [Fe] hydrogenase large subunit. Showing 1 copy in chain B [auth L].
54884
Class: Alpha and beta proteins (a+b)
Fold: Ferredoxin-like
Superfamily: 4Fe-4S ferredoxins
Occurring in:
  1. Periplasmic [Fe] hydrogenase large subunit
The deposited structure of PDB entry 1hfe contains 2 copies of SCOP domain 54884 (Ferredoxin domains from multidomain proteins) in Periplasmic [Fe] hydrogenase large subunit. Showing 1 copy in chain B [auth L].

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