› 2ji6

X-ray diffraction
2.06Å resolution

X-ray structure of Oxalyl-CoA decarboxylase in complex with 3-deaza- ThDP and oxalyl-CoA

Released:
DOI: 10.2210/pdb2ji6/pdb
PDB entry 2ji6 coloured by chain, front view.
PDB entry 2ji6 coloured by chain, side view.
PDB entry 2ji6 coloured by chain, top view.
Source organism: Oxalobacter formigenes
Primary publication:
Crystallographic snapshots of oxalyl-CoA decarboxylase give insights into catalysis by nonoxidative ThDP-dependent decarboxylases.
Berthold CL, Toyota CG, Moussatche P, Wood MD, Leeper F, Richards NG, Lindqvist Y
Structure 15 853-61 (2007)
PMID: 17637344

Function and Biology Details

Reaction catalysed: 
Oxalyl-CoA = formyl-CoA + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-154038 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Oxalyl-CoA decarboxylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 568 amino acids
Theoretical weight: 60.75 KDa
Source organism: Oxalobacter formigenes
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P40149 (Residues: 1-568; Coverage: 100%)
Gene name: oxc
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand TPW 2 x TPW
5 bound ligands:
Ligand MG 2 x MG
Ligand ADP 2 x ADP
Ligand OXK 2 x OXK
Ligand PGE 2 x PGE
Ligand B3P 2 x B3P
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MAX II BEAMLINE I711
Spacegroup: P3121
Unit cell:
a: 127.002Å b: 127.002Å c: 151.813Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.176 0.174 0.212
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Thiamin diphosphate in biological chemistry: analogues of thiamin diphosphate in studies of enzymes and riboswitches.
Agyei-Owusu et al. (2009)
1 more