2D2J

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

2D2J の概要

• エントリーDOI: 10.2210/pdb2d2j/pdb
• 関連するPDBエントリー: 2D2G 2D2H
• 分子名称: phosphotriesterase, COBALT (II) ION, 1,2-ETHANEDIOL, ... (4 entities in total)
• 機能のキーワード: phosphotriesterase, metalloenzyme, opda, hydrolase
• 由来する生物種: Agrobacterium tumefaciens
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 35915.63

構造登録者

Jackson, C.,Kim, H.K.,Carr, P.D.,Liu, J.W.,Ollis, D.L. (登録日: 2005-09-09, 公開日: 2005-09-20, 最終更新日: 2025-03-26)

主引用文献

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

実験手法

X-RAY DIFFRACTION (1.75 Å)