› 5jt1

X-ray diffraction
1.35Å resolution

The 3D structure of Ni-reconstituted U489C variant of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough in the oxidized state at 1.35 Angstrom resolution

Released:
DOI: 10.2210/pdb5jt1/pdb
PDB entry 5jt1 coloured by chain, front view.
PDB entry 5jt1 coloured by chain, side view.
PDB entry 5jt1 coloured by chain, top view.
Source organism: Nitratidesulfovibrio vulgaris str. Hildenborough
Primary publication:
The direct role of selenocysteine in [NiFeSe] hydrogenase maturation and catalysis.
Marques MC, Tapia C, Gutiérrez-Sanz O, Ramos AR, Keller KL, Wall JD, De Lacey AL, Matias PM, Pereira IAC
Nat Chem Biol 13 544-550 (2017)
PMID: 28319099

Function and Biology Details

Reactions catalysed: 
H(2) + 2 ferricytochrome c3 = 2 H(+) + 2 ferrocytochrome c3
H(2) + 2 oxidized ferredoxin = 2 reduced ferredoxin + 2 H(+)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180786 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
cytochrome-c3 hydrogenase Chain: A
Molecule details ›
Chain: A
Length: 317 amino acids
Theoretical weight: 33.94 KDa
Source organism: Nitratidesulfovibrio vulgaris str. Hildenborough
Expression system: Desulfovibrio vulgaris str. Hildenborough
UniProt:
  • Canonical: Q72AS4 (Residues: 1-317; Coverage: 100%)
Gene names: DVU_1917, hysB
Sequence domains:
Structure domains:
Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing Chain: B
Molecule details ›
Chain: B
Length: 507 amino acids
Theoretical weight: 55.93 KDa
Source organism: Nitratidesulfovibrio vulgaris str. Hildenborough
Expression system: Desulfovibrio vulgaris str. Hildenborough
UniProt:
  • Canonical: Q72AS3 (Residues: 12-510; Coverage: 98%)
Gene names: DVU_1918, hysA
Sequence domains: Nickel-dependent hydrogenase
Structure domains: Cytochrome-c3 Hydrogenase, chain B

Ligands and Environments

6 bound ligands:
Ligand SF4 3 x SF4
Ligand 6ML 1 x 6ML
Ligand FCO 1 x FCO
Ligand NI 1 x NI
Ligand FE2 1 x FE2
Ligand H2S 1 x H2S
2 modified residues:
Ligand CSX 1 x CSX
Ligand CSD 1 x CSD

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: C2
Unit cell:
a: 106.778Å b: 63.183Å c: 110.664Å
α: 90° β: 105.27° γ: 90°
R-values:
R R work R free
0.117 0.116 0.145
Expression system: Desulfovibrio vulgaris str. Hildenborough

Quick links

Citations

8 review citations

From protein engineering to artificial enzymes - biological and biomimetic approaches towards sustainable hydrogen production.
Esmieu et al. (2018)
7 more