2d2h

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(New page: 200px<br /><applet load="2d2h" size="350" color="white" frame="true" align="right" spinBox="true" caption="2d2h, resolution 1.80&Aring;" /> '''OpdA from Agrobacter...)
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[[Image:2d2h.gif|left|200px]]<br /><applet load="2d2h" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2d2h, resolution 1.80&Aring;" />
 
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'''OpdA from Agrobacterium radiobacter with bound inhibitor trimethyl phosphate at 1.8 A resolution'''<br />
 
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==Overview==
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==OpdA from Agrobacterium radiobacter with bound inhibitor trimethyl phosphate at 1.8 A resolution==
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A detailed understanding of the catalytic mechanism of enzymes is an, important step toward improving their activity for use in biotechnology., In this paper, crystal soaking experiments and X-ray crystallography were, used to analyse the mechanism of the Agrobacterium radiobacter, phosphotriesterase, OpdA, an enzyme capable of detoxifying a broad range, of organophosphate pesticides. The structures of OpdA complexed with, ethylene glycol and the product of dimethoate hydrolysis, dimethyl, thiophosphate, provide new details of the catalytic mechanism. These, structures suggest that the attacking nucleophile is a terminally bound, hydroxide, consistent with the catalytic mechanism of other binuclear, metallophosphoesterases. In addition, a crystal structure with the, potential substrate trimethyl phosphate bound non-productively, demonstrates the importance of the active site cavity in orienting the, substrate into an approximation of the transition state.
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<StructureSection load='2d2h' size='340' side='right'caption='[[2d2h]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2d2h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D2H 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]] 1.8&#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>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=TZZ:TRIMETHYL+PHOSPHATE'>TZZ</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=2d2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d2h OCA], [https://pdbe.org/2d2h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d2h RCSB], [https://www.ebi.ac.uk/pdbsum/2d2h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d2h ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q93LD7_RHIRD Q93LD7_RHIRD]
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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/d2/2d2h_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=2d2h 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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A detailed understanding of the catalytic mechanism of enzymes is an important step toward improving their activity for use in biotechnology. In this paper, crystal soaking experiments and X-ray crystallography were used to analyse the mechanism of the Agrobacterium radiobacter phosphotriesterase, OpdA, an enzyme capable of detoxifying a broad range of organophosphate pesticides. The structures of OpdA complexed with ethylene glycol and the product of dimethoate hydrolysis, dimethyl thiophosphate, provide new details of the catalytic mechanism. These structures suggest that the attacking nucleophile is a terminally bound hydroxide, consistent with the catalytic mechanism of other binuclear metallophosphoesterases. In addition, a crystal structure with the potential substrate trimethyl phosphate bound non-productively demonstrates the importance of the active site cavity in orienting the substrate into an approximation of the transition state.
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==About this Structure==
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The structure of an enzyme-product complex reveals the critical role of a terminal hydroxide nucleophile in the bacterial phosphotriesterase mechanism.,Jackson C, Kim HK, Carr PD, Liu JW, Ollis DL Biochim Biophys Acta. 2005 Aug 31;1752(1):56-64. PMID:16054447<ref>PMID:16054447</ref>
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2D2H is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens] with <scene name='pdbligand=CO:'>CO</scene>, <scene name='pdbligand=CO2:'>CO2</scene> and <scene name='pdbligand=TZZ:'>TZZ</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Aryldialkylphosphatase Aryldialkylphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.8.1 3.1.8.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2H OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The structure of an enzyme-product complex reveals the critical role of a terminal hydroxide nucleophile in the bacterial phosphotriesterase mechanism., Jackson C, Kim HK, Carr PD, Liu JW, Ollis DL, Biochim Biophys Acta. 2005 Aug 31;1752(1):56-64. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16054447 16054447]
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</div>
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[[Category: Agrobacterium tumefaciens]]
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<div class="pdbe-citations 2d2h" style="background-color:#fffaf0;"></div>
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[[Category: Aryldialkylphosphatase]]
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[[Category: Single protein]]
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[[Category: Carr, P.D.]]
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[[Category: Jackson, C.]]
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[[Category: Kim, H.K.]]
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[[Category: Liu, J.W.]]
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[[Category: Ollis, D.L.]]
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[[Category: CO]]
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[[Category: CO2]]
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[[Category: TZZ]]
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[[Category: metalloenzyme]]
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[[Category: opda]]
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[[Category: phosphotriesterase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 18:53:37 2008''
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==See Also==
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*[[Phosphotriesterase 3D structures|Phosphotriesterase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Agrobacterium tumefaciens]]
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[[Category: Large Structures]]
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[[Category: Carr PD]]
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[[Category: Jackson C]]
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[[Category: Kim HK]]
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[[Category: Liu JW]]
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[[Category: Ollis DL]]

Current revision

OpdA from Agrobacterium radiobacter with bound inhibitor trimethyl phosphate at 1.8 A resolution

PDB ID 2d2h

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