3e3h: Difference between revisions

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-{{Seed}}
-[[Image:3e3h.jpg|left|200px]]
-<!--
+==Crystal structure of the OP hydrolase mutant from Brevundimonas diminuta==
-The line below this paragraph, containing "STRUCTURE_3e3h", creates the "Structure Box" on the page.
+<StructureSection load='3e3h' size='340' side='right'caption='[[3e3h]], [[Resolution|resolution]] 2.15&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'>[[3e3h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Brevundimonas_diminuta Brevundimonas diminuta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E3H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E3H 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]] 2.15&#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=EBP:DIETHYL+4-METHYLBENZYLPHOSPHONATE'>EBP</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
-{{STRUCTURE_3e3h|  PDB=3e3h  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3e3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e3h OCA], [https://pdbe.org/3e3h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e3h RCSB], [https://www.ebi.ac.uk/pdbsum/3e3h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e3h ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/OPD_BREDI OPD_BREDI] Has an unusual substrate specificity for synthetic organophosphate triesters and phosphorofluoridates. All of the phosphate triesters found to be substrates are synthetic compounds. The identity of any naturally occurring substrate for the enzyme is unknown. Has no detectable activity with phosphate monoesters or diesters and no activity as an esterase or protease. It catalyzes the hydrolysis of the insecticide paraoxon at a rate approaching the diffusion limit and thus appears to be optimally evolved for utilizing this synthetic substrate.
+== 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/e3/3e3h_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=3e3h ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Rational site-directed mutagenesis and biophysical analyses have been used to explore the thermodynamic stability and catalytic capabilities of organophosphorus hydrolase (OPH) and its genetically modified variants. There are clear trade-offs in the stability of modifications that enhance catalytic activities. For example, the H254R/H257L variant has higher turnover numbers for the chemical warfare agents VX (144 versus 14 s(-1) for the native enzyme (wild type) and VR (Russian VX, 465 versus 12 s(-1) for wild type). These increases are accompanied by a loss in stability in which the total Gibb's free energy for unfolding is 19.6 kcal/mol, which is 5.7 kcal/mol less than that of the wild-type enzyme. X-ray crystallographic studies support biophysical data that suggest amino acid residues near the active site contribute to the chemical and thermal stability through hydrophobic and cation-pi interactions. The cation-pi interactions appear to contribute an additional 7 kcal/mol to the overall global stability of the enzyme. Using rational design, it has been possible to make amino acid changes in this region that restored the stability, yet maintained effective V-agent activities, with turnover numbers of 68 and 36 s(-1) for VX and VR, respectively. This study describes the first rationally designed, stability/activity balance for an OPH enzyme with a legitimate V-agent activity, and its crystal structure.
-===Crystal structure of the OP hydrolase mutant from Brevundimonas diminuta===
+Balancing the stability and the catalytic specificities of OP hydrolases with enhanced V-agent activities.,Reeves TE, Wales ME, Grimsley JK, Li P, Cerasoli DM, Wild JR Protein Eng Des Sel. 2008 Jun;21(6):405-12. Epub 2008 Apr 23. PMID:18434422<ref>PMID:18434422</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3e3h" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18434422}}, adds the Publication Abstract to the page
+*[[Phosphotriesterase 3D structures|Phosphotriesterase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18434422 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18434422}}
+__TOC__
+</StructureSection>
-==About this Structure==
-E3H is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Brevundimonas_diminuta Brevundimonas diminuta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E3H OCA].
-==Reference==
-Balancing the stability and the catalytic specificities of OP hydrolases with enhanced V-agent activities., Reeves TE, Wales ME, Grimsley JK, Li P, Cerasoli DM, Wild JR, Protein Eng Des Sel. 2008 Jun;21(6):405-12. Epub 2008 Apr 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18434422 18434422]
-[[Category: Aryldialkylphosphatase]]
 [[Category: Brevundimonas diminuta]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Grimsley, J K.]]
+[[Category: Grimsley JK]]
-[[Category: Li, P.]]
+[[Category: Li P]]
-[[Category: Reeves, T E.]]
+[[Category: Reeves TE]]
-[[Category: Wild, J R.]]
+[[Category: Wild JR]]
-[[Category: Membrane]]
-[[Category: Metal-binding]]
-[[Category: Op hydrolase mutant]]
-[[Category: Plasmid]]
-[[Category: Zinc]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct  8 09:32:23 2008''