3d03

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[[Image:3d03.png|left|200px]]
 
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{{STRUCTURE_3d03| PDB=3d03 | SCENE= }}
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==1.9A structure of Glycerophoshphodiesterase (GpdQ) from Enterobacter aerogenes==
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<StructureSection load='3d03' size='340' side='right'caption='[[3d03]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3d03]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_aerogenes Klebsiella aerogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D03 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D03 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3d03 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d03 OCA], [https://pdbe.org/3d03 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d03 RCSB], [https://www.ebi.ac.uk/pdbsum/3d03 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d03 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/GPDQ_KLEAE 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).<ref>PMID:14711669</ref> <ref>PMID:168197</ref> <ref>PMID:17306828</ref> <ref>PMID:17630782</ref> <ref>PMID:18678932</ref> <ref>PMID:18831553</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d0/3d03_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3d03 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===1.9A structure of Glycerophoshphodiesterase (GpdQ) from Enterobacter aerogenes===
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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<ref>PMID:18831553</ref>
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{{ABSTRACT_PUBMED_18831553}}
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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==About this Structure==
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<div class="pdbe-citations 3d03" style="background-color:#fffaf0;"></div>
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[[3d03]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacter_aerogenes Enterobacter aerogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D03 OCA].
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== References ==
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<references/>
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==Reference==
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__TOC__
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<ref group="xtra">PMID:018831553</ref><references group="xtra"/>
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</StructureSection>
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[[Category: Enterobacter aerogenes]]
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[[Category: Klebsiella aerogenes]]
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[[Category: Glycerophosphodiester phosphodiesterase]]
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[[Category: Large Structures]]
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[[Category: Carr, P D.]]
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[[Category: Carr PD]]
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[[Category: Gahan, L R.]]
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[[Category: Gahan LR]]
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[[Category: Guddat, L W.]]
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[[Category: Guddat LW]]
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[[Category: Hadler, K S.]]
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[[Category: Hadler KS]]
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[[Category: Hengge, A C.]]
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[[Category: Hengge AC]]
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[[Category: Jackson, C J.]]
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[[Category: Jackson CJ]]
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[[Category: Larrabee, J A.]]
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[[Category: Larrabee JA]]
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[[Category: Miti, N.]]
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[[Category: Miti N]]
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[[Category: Nguyen, K.]]
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[[Category: Nguyen K]]
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[[Category: Ollis, D L.]]
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[[Category: Ollis DL]]
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[[Category: Schenk, G.]]
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[[Category: Schenk G]]
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[[Category: Tanifum, E.]]
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[[Category: Tanifum E]]
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[[Category: Yip, S H.C.]]
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[[Category: Yip SH-C]]
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[[Category: Glycerophosphodiesterase]]
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[[Category: Hydrolase]]
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[[Category: Metal ion]]
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[[Category: Metallohydrolase]]
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[[Category: Phosphatase]]
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Current revision

1.9A structure of Glycerophoshphodiesterase (GpdQ) from Enterobacter aerogenes

PDB ID 3d03

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