3SO7

Organophoshatedegrading enzyme (OpdA)-phosphate complex

Summary for 3SO7

• Entry DOI: 10.2210/pdb3so7/pdb
• Descriptor: Phosphotriesterase, COBALT (II) ION, SODIUM ION, ... (5 entities in total)
• Functional Keywords: opda, phosphotriesterase, hydrolase
• Biological source: Rhizobium radiobacter (Agrobacterium tumefaciens)
• Total number of polymer chains: 1
• Total formula weight: 35932.45

Authors

Ely, F.,Pedroso, M.,Gahan, L.R.,Ollis, D.L.,Guddat, L.W.,Schenk, G. (deposition date: 2011-06-30, release date: 2011-12-07, Last modification date: 2018-04-18)

Primary citation

Ely, F.,Pedroso, M.M.,Gahan, L.R.,Ollis, D.L.,Guddat, L.W.,Schenk, G.
Phosphate-bound structure of an organophosphate-degrading enzyme from Agrobacterium radiobacter.
J.Inorg.Biochem., 106:19-22, 2011

PubMed Abstract: 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 PO(4) 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 PO(4) is interpreted in terms of a role of the μOH as a reaction nucleophile.

PubMed: 22112835
DOI: 10.1016/j.jinorgbio.2011.09.015

Experimental method

X-RAY DIFFRACTION (2.2 Å)