› 5hi0

X-ray diffraction
2.6Å resolution

The Substrate Binding Mode and Chemical Basis of a Reaction Specificity Switch in Oxalate Decarboxylase

Released:
DOI: 10.2210/pdb5hi0/pdb
PDB entry 5hi0 coloured by chain, front view.
PDB entry 5hi0 coloured by chain, side view.
PDB entry 5hi0 coloured by chain, top view.
Source organism: Bacillus subtilis subsp. subtilis str. 168
Primary publication:
Substrate Binding Mode and Molecular Basis of a Specificity Switch in Oxalate Decarboxylase.
Zhu W, Easthon LM, Reinhardt LA, Tu C, Cohen SE, Silverman DN, Allen KN, Richards NG
Biochemistry 55 2163-73 (2016)
PMID: 27014926

Function and Biology Details

Reaction catalysed: 
Oxalate = formate + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128583 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Oxalate decarboxylase OxdC Chain: A
Molecule details ›
Chain: A
Length: 390 amino acids
Theoretical weight: 44.32 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O34714 (Residues: 1-385; Coverage: 100%)
Gene names: BSU33240, oxdC, yvrK
Sequence domains: Cupin
Structure domains: Jelly Rolls

Ligands and Environments

3 bound ligands:
Ligand CO 2 x CO
Ligand OXL 1 x OXL
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: R32
Unit cell:
a: 154.619Å b: 154.619Å c: 121.954Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.18 0.175 0.224
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Oxygen activation by mononuclear Mn, Co, and Ni centers in biology and synthetic complexes.
Fiedler et al. (2017)
1 more

2 mentions without citation

Substrate Binding Mode and Molecular Basis of a Specificity Switch in Oxalate Decarboxylase.
Zhu et al. (2016)
1 more