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| | ==OpdA from Agrobacterium radiobacter without inhibitor/product present at 1.75 A resolution== | | ==OpdA from Agrobacterium radiobacter without inhibitor/product present at 1.75 A resolution== |
| - | <StructureSection load='2d2j' size='340' side='right' caption='[[2d2j]], [[Resolution|resolution]] 1.75Å' scene=''> | + | <StructureSection load='2d2j' size='340' side='right'caption='[[2d2j]], [[Resolution|resolution]] 1.75Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2d2j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D2J FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2d2j]] 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=2D2J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D2J FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr> | + | <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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2d2g|2d2g]], [[2d2h|2d2h]]</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d2j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d2j OCA], [https://pdbe.org/2d2j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d2j RCSB], [https://www.ebi.ac.uk/pdbsum/2d2j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d2j ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
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| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2d2j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d2j OCA], [http://pdbe.org/2d2j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d2j RCSB], [http://www.ebi.ac.uk/pdbsum/2d2j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2d2j ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q93LD7_RHIRD Q93LD7_RHIRD] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| - | *[[Phosphotriesterase|Phosphotriesterase]] | + | *[[Phosphotriesterase 3D structures|Phosphotriesterase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aryldialkylphosphatase]] | + | [[Category: Agrobacterium tumefaciens]] |
| - | [[Category: Carr, P D]] | + | [[Category: Large Structures]] |
| - | [[Category: Jackson, C]] | + | [[Category: Carr PD]] |
| - | [[Category: Kim, H K]] | + | [[Category: Jackson C]] |
| - | [[Category: Liu, J W]] | + | [[Category: Kim HK]] |
| - | [[Category: Ollis, D L]] | + | [[Category: Liu JW]] |
| - | [[Category: Hydrolase]] | + | [[Category: Ollis DL]] |
| - | [[Category: Metalloenzyme]]
| + | |
| - | [[Category: Opda]]
| + | |
| - | [[Category: Phosphotriesterase]]
| + | |
| Structural highlights
Function
Q93LD7_RHIRD
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
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Jackson C, Kim HK, Carr PD, Liu JW, Ollis DL. The structure of an enzyme-product complex reveals the critical role of a terminal hydroxide nucleophile in the bacterial phosphotriesterase mechanism. Biochim Biophys Acta. 2005 Aug 31;1752(1):56-64. PMID:16054447 doi:http://dx.doi.org/10.1016/j.bbapap.2005.06.008
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