3d03

1.9A structure of Glycerophoshphodiesterase (GpdQ) from Enterobacter aerogenes

spinqualitylabelsall models 3d03, resolution 1.90Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3d03 is a 6 chain structure with sequence from "aerobacter_aerogenes"_hormaeche_and_edwards_1958 "aerobacter aerogenes" hormaeche and edwards 1958. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CO Gene: GPDQ ("Aerobacter aerogenes" Hormaeche and Edwards 1958) Activity: Glycerophosphodiester phosphodiesterase, with EC number 3.1.4.46 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [Q6XBH1_ENTAE] Hydrolyzes cAMP to 5'-AMP. Plays an important regulatory role in modulating the intracellular concentration of cAMP, thereby influencing cAMP-dependent processes.[HAMAP-Rule:MF_00905] 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 glycerophosphodiesterase (GpdQ) from Enterobacter aerogenes is a promiscuous binuclear metallohydrolase that catalyzes the hydrolysis of mono-, di-, and triester substrates, including some organophosphate pesticides and products of the degradation of nerve agents. GpdQ has attracted recent attention as a promising enzymatic bioremediator. Here, we have investigated the catalytic mechanism of this versatile enzyme using a range of techniques. An improved crystal structure (1.9 A resolution) illustrates the presence of (i) an extended hydrogen bond network in the active site, and (ii) two possible nucleophiles, i.e., water/hydroxide ligands, coordinated to one or both metal ions. While it is at present not possible to unambiguously distinguish between these two possibilities, a reaction mechanism is proposed whereby the terminally bound H 2O/OH (-) acts as the nucleophile, activated via hydrogen bonding by the bridging water molecule. Furthermore, the presence of substrate promotes the formation of a catalytically competent binuclear center by significantly enhancing the binding affinity of one of the metal ions in the active site. Asn80 appears to display coordination flexibility that may modulate enzyme activity. Kinetic data suggest that the rate-limiting step occurs after hydrolysis, i.e., the release of the phosphate moiety and the concomitant dissociation of one of the metal ions and/or associated conformational changes. Thus, it is proposed that GpdQ employs an intricate regulatory mechanism for catalysis, where coordination flexibility in one of the two metal binding sites is essential for optimal activity. Substrate-Promoted Formation of a Catalytically Competent Binuclear Center and Regulation of Reactivity in a Glycerophosphodiesterase from Enterobacter aerogenes.,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 J Am Chem Soc. 2008 Oct 3. PMID:18831553 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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