1qb4: Difference between revisions

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 ==CRYSTAL STRUCTURE OF MN(2+)-BOUND PHOSPHOENOLPYRUVATE CARBOXYLASE==
-<StructureSection load='1qb4' size='340' side='right' caption='[[1qb4]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='1qb4' size='340' side='right'caption='[[1qb4]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1qb4]] is a 1 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=1QB4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QB4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1qb4]] is a 1 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=1QB4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QB4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1fiy|1fiy]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">K12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1qb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qb4 OCA], [https://pdbe.org/1qb4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qb4 RCSB], [https://www.ebi.ac.uk/pdbsum/1qb4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qb4 ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoenolpyruvate_carboxylase Phosphoenolpyruvate carboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.31 4.1.1.31] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qb4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qb4 RCSB], [http://www.ebi.ac.uk/pdbsum/1qb4 PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CAPP_ECOLI CAPP_ECOLI]] Forms oxaloacetate, a four-carbon dicarboxylic acid source for the tricarboxylic acid cycle.[HAMAP-Rule:MF_00595]
+[https://www.uniprot.org/uniprot/CAPP_ECOLI CAPP_ECOLI] Forms oxaloacetate, a four-carbon dicarboxylic acid source for the tricarboxylic acid cycle.[HAMAP-Rule:MF_00595]
 == 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/qb/1qb4_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qb/1qb4_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1qb4 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-We have determined the crystal structure of Mn2+-bound Escherichia coli phosphoenolpyruvate carboxylase (PEPC) using X-ray diffraction at 2.6 A resolution, and specified the location of enzyme-bound Mn2+, which is essential for catalytic activity. The electron density map reveals that Mn2+ is bound to the side chain oxygens of Glu-506 and Asp-543, and located at the top of the alpha/beta barrel in PEPC. The coordination sphere of Mn2+ observed in E. coli PEPC is similar to that of Mn2+ found in the pyruvate kinase structure. The model study of Mn2+-bound PEPC complexed with phosphoenolpyruvate (PEP) reveals that the side chains of Arg-396, Arg-581 and Arg-713 could interact with PEP.
-Plausible phosphoenolpyruvate binding site revealed by 2.6 A structure of Mn2+-bound phosphoenolpyruvate carboxylase from Escherichia coli.,Matsumura H, Terada M, Shirakata S, Inoue T, Yoshinaga T, Izui K, Kai Y FEBS Lett. 1999 Sep 17;458(2):93-6. PMID:10481043<ref>PMID:10481043</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
 *[[Phosphoenolpyruvate carboxylase|Phosphoenolpyruvate carboxylase]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Phosphoenolpyruvate carboxylase]]
+[[Category: Large Structures]]
-[[Category: Inoue, T]]
+[[Category: Inoue T]]
-[[Category: Izui, K]]
+[[Category: Izui K]]
-[[Category: Kai, Y]]
+[[Category: Kai Y]]
-[[Category: Matsumura, H]]
+[[Category: Matsumura H]]
-[[Category: Shirakata, S]]
+[[Category: Shirakata S]]
-[[Category: Terada, M]]
+[[Category: Terada M]]
-[[Category: Yoshinaga, T]]
+[[Category: Yoshinaga T]]
-[[Category: Alpha beta barrel]]
-[[Category: Lyase]]