Phosphate-bound structure of an organophosphate-degrading enzyme from Agrobacterium radiobacter

OpdA is a binuclear metalloenzyme that can hydrolyze organophosphate pesticides and nerve agents. In this study the crystal structure of the complex between OpdA and phosphate has been determined to 2.20 Å resolution. The structure shows the phosphate bound in a tripodal mode to the metal ions whereby two of the oxygen atoms of PO4 are terminally bound to each metal ion and a third oxygen bridges the two metal ions, thus displacing the μOH in the active site. In silico modelling demonstrates that the phosphate moiety of a reaction product, e.g. diethyl phosphate, may bind in the same orientation, positioning the diethyl groups neatly into the substrate binding pocket close to the metal center. Thus, similar to the binuclear metallohydrolases urease and purple acid phosphatase the tripodal arrangement of PO4 is interpreted in terms of a role of the μOH as a reaction nucleophile.

Graphical abstractStructure of the OpdA-phosphate complex. The organophosphate-degrading enzyme from Agrobacterium radiobacter (OpdA) is a binuclear metallohydrolase. Addition of phosphate leads to the formation of a tripodal complex whereby the μ-OH is displaced by an oxygen from phosphate, illustrating that the μ-OH may act as a nucleophile during the catalytic cycle.Figure optionsDownload full-size imageDownload as PowerPoint slide