2zo9
Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal ion preference
Structural highlights
FunctionGPDQ_KLEAE Catalyzes the hydrolysis of the 3'-5' phosphodiester bond of glycerophosphodiesters such as glycerophosphorylethanolamine (GPE), a typical phospholipid metabolite which is probably the natural substrate of the enzyme (PubMed:14711669). In addition, exhibits a broad substrate specificity and can catalyze the hydrolysis of various phosphomonoesters, diesters, triesters and phosphothiolates (PubMed:14711669, PubMed:168197, PubMed:17630782). Preferentially hydrolyzes the phosphate diesters over the phosphonate monoesters (PubMed:17630782). Can hydrolyze the model substrates p-nitrophenyl phosphate (pNPP), bis-(p-nitrophenyl phosphate) (bis(pNPP)) and ethyl p-nitrophenyl phosphate (EtpNPP) (PubMed:14711669, PubMed:168197, PubMed:17306828, PubMed:17630782, PubMed:18678932, PubMed:18831553). Also exhibits activity towards some organophosphate pesticides and is capable of hydrolyzing a close analog of EA 2192, the most toxic and persistent degradation product of the nerve agent VX (PubMed:14711669, PubMed:17630782).[1] [2] [3] [4] [5] [6] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe structure of a malonate-bound form of the glycerophosphodiesterase from Enterobacter aerogenes, GpdQ, has been refined at a resolution of 2.2 A to a final R factor of 17.1%. The structure was originally solved to 2.9 A resolution using SAD phases from Zn2+ metal ions introduced into the active site of the apoenzyme [Jackson et al. (2007), J. Mol. Biol. 367, 1047-1062]. However, the 2.9 A resolution was insufficient to discern significant details of the architecture of the binuclear metal centre that constitutes the active site. Furthermore, kinetic analysis revealed that the enzyme lost a significant amount of activity in the presence of Zn2+, suggesting that it is unlikely to be a catalytically relevant metal ion. In this communication, a higher resolution structure of GpdQ is presented in which malonate is visibly coordinated in the active site and analysis of the native metal-ion preference is presented using atomic absorption spectroscopy and anomalous scattering. Catalytic implications of the structure and its Fe2+ metal-ion preference are discussed. Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal-ion preference.,Jackson CJ, Hadler KS, Carr PD, Oakley AJ, Yip S, Schenk G, Ollis DL Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Aug 1;64(Pt, 8):681-5. Epub 2008 Jul 5. PMID:18678932[7] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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