› 2d2j

X-ray diffraction
1.75Å resolution

OpdA from Agrobacterium radiobacter without inhibitor/product present at 1.75 A resolution

Released:
DOI: 10.2210/pdb2d2j/pdb
PDB entry 2d2j coloured by chain, front view.
PDB entry 2d2j coloured by chain, side view.
PDB entry 2d2j coloured by chain, top view.
Source organism: Agrobacterium tumefaciens
Primary publication:
The structure of an enzyme-product complex reveals the critical role of a terminal hydroxide nucleophile in the bacterial phosphotriesterase mechanism.
Jackson C, Kim HK, Carr PD, Liu JW, Ollis DL
Biochim Biophys Acta 1752 56-64 (2005)
PMID: 16054447

Function and Biology Details

Reaction catalysed: 
An aryl dialkyl phosphate + H(2)O = dialkyl phosphate + an aryl alcohol
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188094 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phosphotriesterase Chain: A
Molecule details ›
Chain: A
Length: 329 amino acids
Theoretical weight: 35.67 KDa
Source organism: Agrobacterium tumefaciens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q93LD7 (Residues: 32-360; Coverage: 92%)
Gene name: opdA
Sequence domains: Phosphotriesterase family
Structure domains: Metal-dependent hydrolases

Ligands and Environments

2 bound ligands:
Ligand CO 2 x CO
Ligand EDO 2 x EDO
1 modified residue:
Ligand KCX 1 x KCX

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P3121
Unit cell:
a: 109.242Å b: 109.242Å c: 63.221Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.178 0.172 0.195
Expression system: Escherichia coli

Quick links

Citations

6 review citations

Catalytic mechanisms for phosphotriesterases.
Bigley et al. (2013)
5 more

2 mentions without citation

Enzymatic Bioremediation of Organophosphate Compounds-Progress and Remaining Challenges.
Thakur et al. (2019)
1 more