› 2jib

X-ray diffraction
2.2Å resolution

X-ray structure of Oxalyl-CoA decarboxylase in complex with coenzyme- A

Released:
DOI: 10.2210/pdb2jib/pdb
PDB entry 2jib coloured by chain, front view.
PDB entry 2jib coloured by chain, side view.
PDB entry 2jib 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 TPP 2 x TPP
4 bound ligands:
Ligand MG 2 x MG
Ligand ADP 2 x ADP
Ligand COA 2 x COA
Ligand PGE 2 x PGE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P3121
Unit cell:
a: 127.662Å b: 127.662Å c: 152.074Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.201 0.199 0.238
Expression system: Escherichia coli BL21(DE3)

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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