2D2G: Opda From Agrobacterium Radiobacter With Bound Product Dimethylthiophosphate

A detailed understanding of the catalytic mechanism of enzymes is an important step toward improving their activity for use in biotechnology. In this paper, crystal soaking experiments and X-ray crystallography were used to analyse the mechanism of the Agrobacterium radiobacter phosphotriesterase, OpdA, an enzyme capable of detoxifying a broad range of organophosphate pesticides. The structures of OpdA complexed with ethylene glycol and the product of dimethoate hydrolysis, dimethyl thiophosphate, provide new details of the catalytic mechanism. These structures suggest that the attacking nucleophile is a terminally bound hydroxide, consistent with the catalytic mechanism of other binuclear metallophosphoesterases. In addition, a crystal structure with the potential substrate trimethyl phosphate bound non-productively demonstrates the importance of the active site cavity in orienting the substrate into an approximation of the transition state.
PDB ID: 2D2GDownload
MMDB ID: 35412
PDB Deposition Date: 2005/9/8
Updated in MMDB: 2007/11
Experimental Method:
x-ray diffraction
Resolution: 1.85  Å
Source Organism:
Similar Structures:
Biological Unit for 2D2G: dimeric; determined by author
Molecular Components in 2D2G
Label Count Molecule
Proteins (3 molecules)
Molecule annotation
Chemicals (9 molecules)
Molecule information is not avaliable.
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Citing MMDB