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| | <StructureSection load='2r1k' size='340' side='right'caption='[[2r1k]], [[Resolution|resolution]] 2.10Å' scene=''> | | <StructureSection load='2r1k' size='340' side='right'caption='[[2r1k]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2r1k]] is a 1 chain structure with sequence from [https://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=2R1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R1K FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2r1k]] 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=2R1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R1K FirstGlance]. <br> |
| - | </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=DPF:DIETHYL+HYDROGEN+PHOSPHATE'>DPF</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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]] 2.1Å</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=DPF:DIETHYL+HYDROGEN+PHOSPHATE'>DPF</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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"><div style='overflow: auto; max-height: 3em;'>[[2d2j|2d2j]], [[2d2h|2d2h]], [[2d2g|2d2g]], [[2r1l|2r1l]], [[2r1m|2r1m]], [[2r1n|2r1n]], [[2r1o|2r1o]], [[2r1p|2r1p]]</div></td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">opdA ([https://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>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Aryldialkylphosphatase Aryldialkylphosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.8.1 3.1.8.1] </span></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=2r1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1k OCA], [https://pdbe.org/2r1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r1k RCSB], [https://www.ebi.ac.uk/pdbsum/2r1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r1k ProSAT]</span></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=2r1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1k OCA], [https://pdbe.org/2r1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r1k RCSB], [https://www.ebi.ac.uk/pdbsum/2r1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r1k 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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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aryldialkylphosphatase]] | + | [[Category: Agrobacterium tumefaciens]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Carr, P D]] | + | [[Category: Carr PD]] |
| - | [[Category: Foo, J L]] | + | [[Category: Foo JL]] |
| - | [[Category: Jackson, C J]] | + | [[Category: Jackson CJ]] |
| - | [[Category: Kim, H K]] | + | [[Category: Kim HK]] |
| - | [[Category: Liu, J W]] | + | [[Category: Liu JW]] |
| - | [[Category: Ollis, D L]] | + | [[Category: Ollis DL]] |
| - | [[Category: Salem, G]] | + | [[Category: Salem G]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Metalloenzyme]]
| + | |
| - | [[Category: Opda]]
| + | |
| - | [[Category: Phosphotriesterase]]
| + | |
| Structural highlights
2r1k is a 1 chain structure with sequence from Agrobacterium tumefaciens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.1Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
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
The mechanism by which the binuclear metallophosphotriesterases (PTEs, E.C. 3.1.8.1) catalyse substrate hydrolysis has been extensively studied. The mu-hydroxo bridge between the metal ions has been proposed to be the initiating nucleophile in the hydrolytic reaction. In contrast, analysis of some biomimetic systems has indicated that mu-hydroxo bridges are often not themselves nucleophiles, but act as general bases for freely exchangeable nucleophilic water molecules. Herein, we present crystallographic analyses of a bacterial PTE from Agrobacterium radiobacter, OpdA, capturing the enzyme-substrate complex during hydrolysis. This model of the Michaelis complex suggests the alignment of the substrate will favour attack from a solvent molecule terminally coordinated to the alpha-metal ion. The bridging of both metal ions by the product, without disruption of the mu-hydroxo bridge, is also consistent with nucleophilic attack occurring from the terminal position. When phosphodiesters are soaked into crystals of OpdA, they coordinate bidentately to the beta-metal ion, displacing the mu-hydroxo bridge. Thus, alternative product-binding modes exist for the PTEs, and it is the bridging mode that appears to result from phosphotriester hydrolysis. Kinetic analysis of the PTE and promiscuous phosphodiesterase activities confirms that the presence of a mu-hydroxo bridge during phosphotriester hydrolysis is correlated with a lower pK(a) for the nucleophile, consistent with a general base function during catalysis.
In crystallo capture of a Michaelis complex and product-binding modes of a bacterial phosphotriesterase.,Jackson CJ, Foo JL, Kim HK, Carr PD, Liu JW, Salem G, Ollis DL J Mol Biol. 2008 Feb 1;375(5):1189-96. Epub 2007 Nov 1. PMID:18082180[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Jackson CJ, Foo JL, Kim HK, Carr PD, Liu JW, Salem G, Ollis DL. In crystallo capture of a Michaelis complex and product-binding modes of a bacterial phosphotriesterase. J Mol Biol. 2008 Feb 1;375(5):1189-96. Epub 2007 Nov 1. PMID:18082180 doi:http://dx.doi.org/10.1016/j.jmb.2007.10.061
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