2D2J

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

Summary for 2D2J

• Entry DOI: 10.2210/pdb2d2j/pdb
• Related: 2D2G 2D2H
• Descriptor: phosphotriesterase, COBALT (II) ION, 1,2-ETHANEDIOL, ... (4 entities in total)
• Functional Keywords: phosphotriesterase, metalloenzyme, opda, hydrolase
• Biological source: Agrobacterium tumefaciens
• Total number of polymer chains: 1
• Total formula weight: 35915.63

Authors

Jackson, C.,Kim, H.K.,Carr, P.D.,Liu, J.W.,Ollis, D.L. (deposition date: 2005-09-09, release date: 2005-09-20, Last modification date: 2015-08-19)

Primary citation

Jackson, C.,Kim, H.K.,Carr, P.D.,Liu, J.W.,Ollis, D.L.
The structure of an enzyme-product complex reveals the critical role of a terminal hydroxide nucleophile in the bacterial phosphotriesterase mechanism
Biochim.Biophys.Acta, 1752:56-64, 2005

PubMed Abstract: 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.

PubMed: 16054447
DOI: 10.1016/j.bbapap.2005.06.008

Experimental method

X-RAY DIFFRACTION (1.75 Å)