› 4ucq

X-ray diffraction
2.6Å resolution

Structure of the T18D small subunit mutant of D. fructosovorans NiFe- hydrogenase

Released:
DOI: 10.2210/pdb4ucq/pdb
PDB entry 4ucq coloured by chain, front view.
PDB entry 4ucq coloured by chain, side view.
PDB entry 4ucq coloured by chain, top view.
Source organism: Solidesulfovibrio fructosivorans
Primary publication:
A threonine stabilizes the NiC and NiR catalytic intermediates of [NiFe]-hydrogenase.
Abou-Hamdan A, Ceccaldi P, Lebrette H, Gutiérrez-Sanz O, Richaud P, Cournac L, Guigliarelli B, De Lacey AL, Léger C, Volbeda A, Burlat B, Dementin S
J Biol Chem 290 8550-8 (2015)
PMID: 25666617

Function and Biology Details

Reaction catalysed: 
H(2) + 2 ferricytochrome c3 = 2 H(+) + 2 ferrocytochrome c3
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-148312 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Periplasmic [NiFe] hydrogenase small subunit Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 264 amino acids
Theoretical weight: 28.36 KDa
Source organism: Solidesulfovibrio fructosivorans
Expression system: Solidesulfovibrio fructosivorans JJ]
UniProt:
  • Canonical: P18187 (Residues: 51-314; Coverage: 100%)
Gene name: hydA
Sequence domains:
Structure domains:
Periplasmic [NiFe] hydrogenase large subunit Chains: Q, R, S
Molecule details ›
Chains: Q, R, S
Length: 563 amino acids
Theoretical weight: 61.2 KDa
Source organism: Solidesulfovibrio fructosivorans
Expression system: Solidesulfovibrio fructosivorans JJ]
UniProt:
  • Canonical: P18188 (Residues: 2-549; Coverage: 97%)
Gene name: hydB
Sequence domains: Nickel-dependent hydrogenase
Structure domains: Cytochrome-c3 Hydrogenase, chain B

Ligands and Environments

6 bound ligands:
Ligand SF4 6 x SF4
Ligand F3S 3 x F3S
Ligand GOL 6 x GOL
Ligand FCO 3 x FCO
Ligand NI 3 x NI
Ligand MG 3 x MG
1 modified residue:
Ligand CSX 3 x CSX

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P21
Unit cell:
a: 63.8Å b: 99.9Å c: 183.3Å
α: 90° β: 91.9° γ: 90°
R-values:
R R work R free
0.2 0.198 0.241
Expression system: Solidesulfovibrio fructosivorans JJ]

Quick links

Citations

5 review citations

Structure and function of [NiFe] hydrogenases.
Ogata et al. (2016)
4 more

1 mention without citation

A threonine stabilizes the NiC and NiR catalytic intermediates of [NiFe]-hydrogenase.
Abou-Hamdan et al. (2015)