2qta: Difference between revisions

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-[[Image:2qta.png|left|200px]]
-<!--
+==E. coli Pyruvate dehydrogenase E1 component E401K mutant with thiamin diphosphate==
-The line below this paragraph, containing "STRUCTURE_2qta", creates the "Structure Box" on the page.
+<StructureSection load='2qta' size='340' side='right'caption='[[2qta]], [[Resolution|resolution]] 1.85&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'>[[2qta]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QTA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QTA 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]] 1.85&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
-{{STRUCTURE_2qta|  PDB=2qta  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2qta FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qta OCA], [https://pdbe.org/2qta PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qta RCSB], [https://www.ebi.ac.uk/pdbsum/2qta PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qta ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ODP1_ECOLI ODP1_ECOLI] Component of the pyruvate dehydrogenase (PDH) complex, that catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2).
+== 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/qt/2qta_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=2qta ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Our crystallographic studies have shown that two active center loops (an inner loop formed by residues 401-413 and outer loop formed by residues 541-557) of the E1 component of the Escherichia coli pyruvate dehydrogenase complex become organized only on binding a substrate analog that is capable of forming a stable thiamin diphosphate-bound covalent intermediate. We showed that residue His-407 on the inner loop has a key role in the mechanism, especially in the reductive acetylation of the E. coli dihydrolipoamide transacetylase component, whereas crystallographic results showed a role of this residue in a disorder-order transformation of these two loops, and the ordered conformation gives rise to numerous new contacts between the inner loop and the active center. We present mapping of the conserved residues on the inner loop. Kinetic, spectroscopic, and crystallographic studies on some inner loop variants led us to conclude that charged residues flanking His-407 are important for stabilization/ordering of the inner loop thereby facilitating completion of the active site. The results further suggest that a disorder to order transition of the dynamic inner loop is essential for substrate entry to the active site, for sequestering active site chemistry from undesirable side reactions, as well as for communication between the E1 and E2 components of the E. coli pyruvate dehydrogenase multienzyme complex.
-===E. coli Pyruvate dehydrogenase E1 component E401K mutant with thiamin diphosphate===
+A dynamic loop at the active center of the Escherichia coli pyruvate dehydrogenase complex E1 component modulates substrate utilization and chemical communication with the E2 component.,Kale S, Arjunan P, Furey W, Jordan F J Biol Chem. 2007 Sep 21;282(38):28106-16. Epub 2007 Jul 17. PMID:17635929<ref>PMID:17635929</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_17635929}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2qta" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 17635929 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_17635929}}
-==About this Structure==
-[[2qta]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QTA OCA].
 ==See Also==
-*[[Pyruvate dehydrogenase]]
+*[[Pyruvate dehydrogenase 3D structures|Pyruvate dehydrogenase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:017635929</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Arjunan, P.]]
+[[Category: Large Structures]]
-[[Category: Chandrasekhar, K.]]
+[[Category: Arjunan P]]
-[[Category: Furey, W.]]
+[[Category: Chandrasekhar K]]
-[[Category: Glycolysis]]
+[[Category: Furey W]]
-[[Category: Magnesium]]
-[[Category: Metal-binding]]
-[[Category: Oxidoreductase]]
-[[Category: Pyruvate dehydrogenase]]
-[[Category: Thiamin diphosphate]]
-[[Category: Thiamine pyrophosphate]]