› 8pow

X-ray diffraction
1.61Å resolution

Crystal Structure of the C19G variant of the membrane-bound [NiFe]-Hydrogenase from Cupriavidus necator in the air-oxidized state at 1.61 A Resolution.

Released:
DOI: 10.2210/pdb8pow/pdb
Model geometry
Fit model/data
PDB entry 8pow coloured by chain, front view.
PDB entry 8pow coloured by chain, side view.
PDB entry 8pow coloured by chain, top view.
Source organism: Cupriavidus necator H16
Primary publication:
Stepwise conversion of the Cys6[4Fe-3S] to a Cys4[4Fe-4S] cluster and its impact on the oxygen tolerance of [NiFe]-hydrogenase.
Schmidt A, Kalms J, Lorent C, Katz S, Frielingsdorf S, Evans RM, Fritsch J, Siebert E, Teutloff C, Armstrong FA, Zebger I, Lenz O, Scheerer P
OpenAccess logo Chem Sci 14 11105-11120 (2023)
PMID: 37860641

Function and Biology Details

Reaction catalysed: 
H(2) + A = AH(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152104 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Uptake hydrogenase large subunit Chain: L
Molecule details ›
Chain: L
Length: 603 amino acids
Theoretical weight: 67.26 KDa
Source organism: Cupriavidus necator H16
Expression system: Cupriavidus necator H16
UniProt:
  • Canonical: P31891 (Residues: 1-603; Coverage: 98%)
Gene names: PHG002, hoxG
Sequence domains: Nickel-dependent hydrogenase
Uptake hydrogenase small subunit Chain: S
Molecule details ›
Chain: S
Length: 328 amino acids
Theoretical weight: 35.98 KDa
Source organism: Cupriavidus necator H16
Expression system: Cupriavidus necator H16
UniProt:
  • Canonical: P31892 (Residues: 44-360; Coverage: 100%)
Gene names: PHG001, hoxK
Sequence domains:

Ligands and Environments

6 bound ligands:
Ligand NFV 1 x NFV
Ligand MG 1 x MG
Ligand CL 3 x CL
Ligand SF4 1 x SF4
Ligand F3S 1 x F3S
Ligand ER2 1 x ER2
1 modified residue:
Ligand CSO 1 x CSO

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P212121
Unit cell:
a: 72.526Å b: 95.523Å c: 118.868Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.138 0.137 0.163
Expression system: Cupriavidus necator H16

Quick links

Citations

1 review citation

Outer-sphere effects on the O2 sensitivity, catalytic bias and catalytic reversibility of hydrogenases.
Fasano et al. (2024)

1 mention without citation

Stepwise conversion of the Cys6[4Fe-3S] to a Cys4[4Fe-4S] cluster and its impact on the oxygen tolerance of [NiFe]-hydrogenase.
Schmidt et al. (2023)