› 3f6b

X-ray diffraction
1.34Å resolution

Crystal structure of benzoylformate decarboxylase in complex with the pyridyl inhibitor PAA

Released:
DOI: 10.2210/pdb3f6b/pdb
PDB entry 3f6b coloured by chain, front view.
PDB entry 3f6b coloured by chain, side view.
PDB entry 3f6b coloured by chain, top view.
Source organism: Pseudomonas putida
Primary publication:
Detection and time course of formation of major thiamin diphosphate-bound covalent intermediates derived from a chromophoric substrate analogue on benzoylformate decarboxylase.
Chakraborty S, Nemeria NS, Balakrishnan A, Brandt GS, Kneen MM, Yep A, McLeish MJ, Kenyon GL, Petsko GA, Ringe D, Jordan F
Biochemistry 48 981-94 (2009)
PMID: 19140682

Function and Biology Details

Reaction catalysed: 
Benzoylformate = benzaldehyde + CO(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149084 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Benzoylformate decarboxylase Chain: X
Molecule details ›
Chain: X
Length: 525 amino acids
Theoretical weight: 56.04 KDa
Source organism: Pseudomonas putida
Expression system: Escherichia coli
UniProt:
  • Canonical: P20906 (Residues: 2-526; Coverage: 99%)
Gene name: mdlC
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand 8PA 1 x 8PA
1 bound ligand:
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: I222
Unit cell:
a: 81.54Å b: 96.07Å c: 137.354Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.167 0.162 0.182
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Reaction mechanisms of thiamin diphosphate enzymes: defining states of ionization and tautomerization of the cofactor at individual steps.
Nemeria et al. (2009)
2 more

1 mention without citation

Detection and time course of formation of major thiamin diphosphate-bound covalent intermediates derived from a chromophoric substrate analogue on benzoylformate decarboxylase.
Chakraborty et al. (2009)