2zo9

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Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal ion preferenceMalonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal ion preference

Structural highlights

2zo9 is a 2 chain structure with sequence from Klebsiella aerogenes. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GPDQ_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 PubMed

The 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 Also

References

  1. ↑ McLoughlin SY, Jackson C, Liu JW, Ollis DL. Growth of Escherichia coli coexpressing phosphotriesterase and glycerophosphodiester phosphodiesterase, using paraoxon as the sole phosphorus source. Appl Environ Microbiol. 2004 Jan;70(1):404-12. PMID:14711669 doi:10.1128/AEM.70.1.404-412.2004
  2. ↑ Gerlt JA, Whitman GJ. Purification and properties of a phosphohydrolase from Enterobacter aerogenes. J Biol Chem. 1975 Jul 10;250(13):5053-8 PMID:168197
  3. ↑ Jackson CJ, Carr PD, Liu JW, Watt SJ, Beck JL, Ollis DL. The structure and function of a novel glycerophosphodiesterase from Enterobacter aerogenes. J Mol Biol. 2007 Apr 6;367(4):1047-62. Epub 2007 Jan 20. PMID:17306828 doi:10.1016/j.jmb.2007.01.032
  4. ↑ Ghanem E, Li Y, Xu C, Raushel FM. Characterization of a phosphodiesterase capable of hydrolyzing EA 2192, the most toxic degradation product of the nerve agent VX. Biochemistry. 2007 Aug 7;46(31):9032-40. PMID:17630782 doi:10.1021/bi700561k
  5. ↑ Jackson CJ, Hadler KS, Carr PD, Oakley AJ, Yip S, Schenk G, Ollis DL. Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal-ion preference. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Aug 1;64(Pt, 8):681-5. Epub 2008 Jul 5. PMID:18678932 doi:10.1107/S1744309108017600
  6. ↑ Hadler KS, Tanifum EA, Yip SH, Mitic N, Guddat LW, Jackson CJ, Gahan LR, Nguyen K, Carr PD, Ollis DL, Hengge AC, Larrabee JA, Schenk G. Substrate-Promoted Formation of a Catalytically Competent Binuclear Center and Regulation of Reactivity in a Glycerophosphodiesterase from Enterobacter aerogenes. J Am Chem Soc. 2008 Oct 3. PMID:18831553 doi:http://dx.doi.org/10.1021/ja803346w
  7. ↑ Jackson CJ, Hadler KS, Carr PD, Oakley AJ, Yip S, Schenk G, Ollis DL. Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal-ion preference. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Aug 1;64(Pt, 8):681-5. Epub 2008 Jul 5. PMID:18678932 doi:10.1107/S1744309108017600

2zo9, resolution 2.20Å

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