1oy0: Difference between revisions

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 ==The crystal Structure of the First Enzyme of Pantothenate Biosynthetic Pathway, Ketopantoate Hydroxymethyltransferase from Mycobacterium Tuberculosis Shows a Decameric Assembly and Terminal Helix-Swapping==
-<StructureSection load='1oy0' size='340' side='right' caption='[[1oy0]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='1oy0' size='340' side='right'caption='[[1oy0]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1oy0]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OY0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OY0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1oy0]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OY0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OY0 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.8&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PANB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-methyl-2-oxobutanoate_hydroxymethyltransferase 3-methyl-2-oxobutanoate hydroxymethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.11 2.1.2.11] </span></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=1oy0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oy0 OCA], [https://pdbe.org/1oy0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oy0 RCSB], [https://www.ebi.ac.uk/pdbsum/1oy0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oy0 ProSAT]</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=1oy0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oy0 OCA], [http://pdbe.org/1oy0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1oy0 RCSB], [http://www.ebi.ac.uk/pdbsum/1oy0 PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PANB_MYCTU PANB_MYCTU]] Catalyzes the reversible reaction in which hydroxymethyl group from 5,10-methylenetetrahydrofolate is tranferred onto alpha-ketoisovalerate to form ketopantoate.<ref>PMID:12515554</ref>
+[https://www.uniprot.org/uniprot/PANB_MYCTU PANB_MYCTU] Catalyzes the reversible reaction in which hydroxymethyl group from 5,10-methylenetetrahydrofolate is tranferred onto alpha-ketoisovalerate to form ketopantoate.<ref>PMID:12515554</ref>
 == 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/oy/1oy0_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oy/1oy0_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 20: / Line 20: @@
 </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=1oy0 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate, which is a precursor to coenzyme A and is required for penicillin biosynthesis. The crystal structure of KPHMT from Mycobacterium tuberculosis was determined by the single anomalous substitution (SAS) method at 2.8 A resolution. KPHMT adopts a structure that is a variation on the (beta/alpha) barrel fold, with a metal binding site proximal to the presumed catalytic site. The protein forms a decameric complex, with subunits in opposing pentameric rings held together by a swapping of their C-terminal alpha helices. The structure reveals KPHMT's membership in a small, recently discovered group of (beta/alpha) barrel enzymes that employ domain swapping to form a variety of oligomeric assemblies. The apparent conservation of certain detailed structural characteristics suggests that KPHMT is distantly related by divergent evolution to enzymes in unrelated pathways, including isocitrate lyase and phosphoenolpyruvate mutase.
-The crystal structure of the first enzyme in the pantothenate biosynthetic pathway, ketopantoate hydroxymethyltransferase, from M tuberculosis.,Chaudhuri BN, Sawaya MR, Kim CY, Waldo GS, Park MS, Terwilliger TC, Yeates TO Structure. 2003 Jul;11(7):753-64. PMID:12842039<ref>PMID:12842039</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1oy0" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: 3-methyl-2-oxobutanoate hydroxymethyltransferase]]
+[[Category: Large Structures]]
-[[Category: Chaudhuri, B N]]
+[[Category: Mycobacterium tuberculosis]]
-[[Category: Kim, C Y]]
+[[Category: Chaudhuri BN]]
-[[Category: Park, M S]]
+[[Category: Kim CY]]
-[[Category: Sawaya, M R]]
+[[Category: Park MS]]
-[[Category: Structural genomic]]
+[[Category: Sawaya MR]]
-[[Category: Terwilliger, T C]]
+[[Category: Terwilliger TC]]
-[[Category: Waldo, G S]]
+[[Category: Waldo GS]]
-[[Category: Yeates, T O]]
+[[Category: Yeates TO]]
-[[Category: Domain swapping]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Tbsgc]]
-[[Category: Transferase]]