2d2h: Difference between revisions

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-{{Seed}}
-[[Image:2d2h.png|left|200px]]
-<!--
+==OpdA from Agrobacterium radiobacter with bound inhibitor trimethyl phosphate at 1.8 A resolution==
-The line below this paragraph, containing "STRUCTURE_2d2h", creates the "Structure Box" on the page.
+<StructureSection load='2d2h' size='340' side='right'caption='[[2d2h]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</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>
--->
+<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>
-{{STRUCTURE_2d2h|  PDB=2d2h  |  SCENE=  }}
+<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>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q93LD7_RHIRD Q93LD7_RHIRD]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d2/2d2h_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== 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.
-===OpdA from Agrobacterium radiobacter with bound inhibitor trimethyl phosphate at 1.8 A resolution===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2d2h" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16054447}}, adds the Publication Abstract to the page
+*[[Phosphotriesterase 3D structures|Phosphotriesterase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16054447 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16054447}}
+__TOC__
+</StructureSection>
-==About this Structure==
-D2H is a [[Single protein]] structure of sequence from [http://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].
-==Reference==
-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://www.ncbi.nlm.nih.gov/pubmed/16054447 16054447]
 [[Category: Agrobacterium tumefaciens]]
-[[Category: Aryldialkylphosphatase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Carr PD]]
-[[Category: Carr, P D.]]
+[[Category: Jackson C]]
-[[Category: Jackson, C.]]
+[[Category: Kim HK]]
-[[Category: Kim, H K.]]
+[[Category: Liu JW]]
-[[Category: Liu, J W.]]
+[[Category: Ollis DL]]
-[[Category: Ollis, D L.]]
-[[Category: Metalloenzyme]]
-[[Category: Opda]]
-[[Category: Phosphotriesterase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 22:55:43 2008''