2r1m

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(New page: 200px<br /><applet load="2r1m" size="350" color="white" frame="true" align="right" spinBox="true" caption="2r1m, resolution 2.50&Aring;" /> '''OpdA from Agrobacter...)
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[[Image:2r1m.jpg|left|200px]]<br /><applet load="2r1m" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2r1m, resolution 2.50&Aring;" />
 
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'''OpdA from Agrobacterium radiobacter with bound product diethyl phosphate from crystal soaking with diethyl 4-methoxyphenyl phosphate (450h)- 2.5 A'''<br />
 
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==Overview==
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==OpdA from Agrobacterium radiobacter with bound product diethyl phosphate from crystal soaking with diethyl 4-methoxyphenyl phosphate (450h)- 2.5 A==
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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.
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<StructureSection load='2r1m' size='340' side='right'caption='[[2r1m]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2r1m]] 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=2R1M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R1M 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]] 2.5&#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=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>
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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=2r1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1m OCA], [https://pdbe.org/2r1m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r1m RCSB], [https://www.ebi.ac.uk/pdbsum/2r1m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r1m 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/r1/2r1m_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2r1m 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 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.
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==About this Structure==
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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<ref>PMID:18082180</ref>
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2R1M 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=FE2:'>FE2</scene>, <scene name='pdbligand=CO:'>CO</scene>, <scene name='pdbligand=DPF:'>DPF</scene> and <scene name='pdbligand=EDO:'>EDO</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] Known structural/functional Sites: <scene name='pdbsite=AC1:Fe2+Binding+Site+For+Residue+A+800'>AC1</scene>, <scene name='pdbsite=AC2:Co+Binding+Site+For+Residue+A+801'>AC2</scene>, <scene name='pdbsite=AC3:Dpf+Binding+Site+For+Residue+A+1'>AC3</scene> and <scene name='pdbsite=AC4:Edo+Binding+Site+For+Residue+A+701'>AC4</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1M 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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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18082180 18082180]
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</div>
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[[Category: Agrobacterium tumefaciens]]
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<div class="pdbe-citations 2r1m" 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: Foo, J.L.]]
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[[Category: Jackson, C.J.]]
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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: Salem, G.]]
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[[Category: CO]]
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[[Category: DPF]]
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[[Category: EDO]]
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[[Category: FE2]]
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[[Category: hydrolase]]
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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 Wed Feb 13 08:21:17 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: Foo JL]]
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[[Category: Jackson CJ]]
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[[Category: Kim HK]]
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[[Category: Liu JW]]
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[[Category: Ollis DL]]
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[[Category: Salem G]]

Current revision

OpdA from Agrobacterium radiobacter with bound product diethyl phosphate from crystal soaking with diethyl 4-methoxyphenyl phosphate (450h)- 2.5 A

PDB ID 2r1m

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