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| | ==Structure of OpdA mutant Y257F== | | ==Structure of OpdA mutant Y257F== |
| - | <StructureSection load='3oqe' size='340' side='right' caption='[[3oqe]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='3oqe' size='340' side='right'caption='[[3oqe]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3oqe]] 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=3OQE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OQE FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3oqe]] 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=3OQE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OQE 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]] 1.9Å</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">[[3ood|3ood]]</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=3oqe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oqe OCA], [https://pdbe.org/3oqe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3oqe RCSB], [https://www.ebi.ac.uk/pdbsum/3oqe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3oqe ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">opdA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 "Achromobacter radiobacter" (Beijerinck and van Delden 1902) Bergey et al. 1934])</td></tr>
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| - | <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=3oqe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oqe OCA], [http://pdbe.org/3oqe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3oqe RCSB], [http://www.ebi.ac.uk/pdbsum/3oqe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3oqe ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q93LD7_RHIRD Q93LD7_RHIRD] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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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: Ely, F]] | + | [[Category: Large Structures]] |
| - | [[Category: Guddat, L W]] | + | [[Category: Ely F]] |
| - | [[Category: Ollis, D L]] | + | [[Category: Guddat LW]] |
| - | [[Category: Schenk, G]] | + | [[Category: Ollis DL]] |
| - | [[Category: Divalent metal ion]] | + | [[Category: Schenk G]] |
| - | [[Category: Hydrolase]]
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| - | [[Category: Organophosphate]]
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| - | [[Category: Phosphotriesterase]]
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| - | [[Category: Tim barrel]]
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| Structural highlights
Function
Q93LD7_RHIRD
Publication Abstract from PubMed
The OP (organophosphate)-degrading enzyme from Agrobacterium radiobacter (OpdA) is a binuclear metallohydrolase able to degrade highly toxic OP pesticides and nerve agents into less or non-toxic compounds. In the present study, the effect of metal ion substitutions and site-directed mutations on the catalytic properties of OpdA are investigated. The study shows the importance of both the metal ion composition and a hydrogen-bond network that connects the metal ion centre with the substrate-binding pocket using residues Arg254 and Tyr257 in the mechanism and substrate specificity of this enzyme. For the Co(II) derivative of OpdA two protonation equilibria (pKa1 ~5; pKa2 ~10) have been identified as relevant for catalysis, and a terminal hydroxide acts as the likely hydrolysis-initiating nucleophile. In contrast, the Zn(II) and Cd(II) derivatives only have one relevant protonation equilibrium (pKa ~4-5), and the muOH is the proposed nucleophile. The observed mechanistic flexibility may reconcile contrasting reaction models that have been published previously and may be beneficial for the rapid adaptation of OP-degrading enzymes to changing environmental pressures.
The organophosphate-degrading enzyme from Agrobacterium radiobacter displays mechanistic flexibility for catalysis.,Ely F, Hadler KS, Gahan LR, Guddat LW, Ollis DL, Schenk G Biochem J. 2010 Nov 25;432(3):565-73. PMID:20868365[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Ely F, Hadler KS, Gahan LR, Guddat LW, Ollis DL, Schenk G. The organophosphate-degrading enzyme from Agrobacterium radiobacter displays mechanistic flexibility for catalysis. Biochem J. 2010 Nov 25;432(3):565-73. PMID:20868365 doi:10.1042/BJ20101054
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