2ptz: Difference between revisions

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-[[Image:2ptz.png|left|200px]]
-<!--
+==Crystal Structure of the T. brucei enolase complexed with phosphonoacetohydroxamate (PAH), His156-out conformation==
-The line below this paragraph, containing "STRUCTURE_2ptz", creates the "Structure Box" on the page.
+<StructureSection load='2ptz' size='340' side='right'caption='[[2ptz]], [[Resolution|resolution]] 1.65&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'>[[2ptz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_brucei Trypanosoma brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PTZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PTZ 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]] 1.65&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PAH:PHOSPHONOACETOHYDROXAMIC+ACID'>PAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2ptz|  PDB=2ptz  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ptz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ptz OCA], [https://pdbe.org/2ptz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ptz RCSB], [https://www.ebi.ac.uk/pdbsum/2ptz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ptz ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q38BV6_TRYB2 Q38BV6_TRYB2]
+== 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/pt/2ptz_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=2ptz ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Enolase is a validated drug target in Trypanosoma brucei. To better characterize its properties and guide drug design efforts, we have determined six new crystal structures of the enzyme, in various ligation states and conformations, and have carried out complementary molecular dynamics simulations. The results show a striking structural diversity of loops near the catalytic site, for which variation can be interpreted as distinct modes of conformational variability that are explored during the molecular dynamics simulations. Our results show that sulfate may, unexpectedly, induce full closure of catalytic site loops whereas, conversely, binding of inhibitor phosphonoacetohydroxamate may leave open a tunnel from the catalytic site to protein surface offering possibilities for drug development. We also present the first complex of enolase with a novel inhibitor 2-fluoro-2-phosphonoacetohydroxamate. The molecular dynamics results further encourage efforts to design irreversible species-specific inhibitors: they reveal that a parasite enzyme-specific lysine may approach the catalytic site more closely than crystal structures suggest and also cast light on the issue of accessibility of parasite enzyme-specific cysteines to chemically modifying reagents. One of the new sulfate structures contains a novel metal-binding site IV within the catalytic site cleft.
-===Crystal Structure of the T. brucei enolase complexed with phosphonoacetohydroxamate (PAH), His156-out conformation===
+Structural flexibility in Trypanosoma brucei enolase revealed by X-ray crystallography and molecular dynamics.,de A S Navarro MV, Gomes Dias SM, Mello LV, da Silva Giotto MT, Gavalda S, Blonski C, Garratt RC, Rigden DJ FEBS J. 2007 Oct;274(19):5077-89. Epub 2007 Sep 5. PMID:17822439<ref>PMID:17822439</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_17822439}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2ptz" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 17822439 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_17822439}}
-==About this Structure==
-[[2ptz]] is a 1 chain structure of [[Enolase]] with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei Trypanosoma brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PTZ OCA].
 ==See Also==
-*[[Enolase|Enolase]]
+*[[Enolase 3D structures|Enolase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:017822439</ref><ref group="xtra">PMID:012899835</ref><references group="xtra"/>
+__TOC__
-[[Category: Phosphopyruvate hydratase]]
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Trypanosoma brucei]]
-[[Category: Dias, S M.G.]]
+[[Category: Dias SMG]]
-[[Category: Garratt, R C.]]
+[[Category: Garratt RC]]
-[[Category: Navarro, M V.A S.]]
+[[Category: Navarro MVAS]]
-[[Category: Rigden, D J.]]
+[[Category: Rigden DJ]]
-[[Category: Glycolysis]]
-[[Category: His-tag]]
-[[Category: Lyase]]