1pt5: Difference between revisions

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-[[Image:1pt5.jpg|left|200px]]<br /><applet load="1pt5" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1pt5, resolution 2.00&Aring;" />
-'''Crystal structure of gene yfdW of E. coli'''<br />
-==Overview==
+==Crystal structure of gene yfdW of E. coli==
-Because of its toxicity, oxalate accumulation from amino acid catabolism leads to acute disorders in mammals. Gut microflora are therefore pivotal in maintaining a safe intestinal oxalate balance through oxalate degradation. Oxalate catabolism was first identified in Oxalobacter formigenes, a specialized, strictly anaerobic bacterium. Oxalate degradation was found to be performed successively by two enzymes, a formyl-CoA transferase (frc) and an oxalate decarboxylase (oxc). These two genes are present in several bacterial genomes including that of Escherichia coli. The frc ortholog in E. coli is yfdW, with which it shares 61% sequence identity. We have expressed the YfdW open reading frame product and solved its crystal structure in the apo-form and in complex with acetyl-CoA and with a mixture of acetyl-CoA and oxalate. YfdW exhibits a novel and spectacular fold in which two monomers assemble as interlaced rings, defining the CoA binding site at their interface. From the structure of the complex with acetyl-CoA and oxalate, we propose a putative formyl/oxalate transfer mechanism involving the conserved catalytic residue Asp169. The similarity of yfdW with bacterial orthologs (approximately 60% identity) and paralogs (approximately 20-30% identity) suggests that this new fold and parts of the CoA transfer mechanism are likely to be the hallmarks of a wide family of CoA transferases.
+<StructureSection load='1pt5' size='340' side='right'caption='[[1pt5]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1pt5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Shigella_flexneri Shigella flexneri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PT5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PT5 FirstGlance]. <br>
-PT5 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli,_and_shigella_flexneri Escherichia coli, and shigella flexneri] with <scene name='pdbligand=ACO:'>ACO</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PT5 OCA].
+</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&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACO:ACETYL+COENZYME+*A'>ACO</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pt5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pt5 OCA], [https://pdbe.org/1pt5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pt5 RCSB], [https://www.ebi.ac.uk/pdbsum/1pt5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pt5 ProSAT]</span></td></tr>
-The crystal structure of the Escherichia coli YfdW gene product reveals a new fold of two interlaced rings identifying a wide family of CoA transferases., Gruez A, Roig-Zamboni V, Valencia C, Campanacci V, Cambillau C, J Biol Chem. 2003 Sep 5;278(36):34582-6. Epub 2003 Jul 3. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12844490 12844490]
+</table>
-[[Category: Escherichia coli, and shigella flexneri]]
+== Function ==
-[[Category: Single protein]]
+[https://www.uniprot.org/uniprot/FCTA_ECOLI FCTA_ECOLI] Catalyzes the transfer of the CoA moiety from formyl-CoA to oxalate.
-[[Category: Cambillau, C.]]
+== Evolutionary Conservation ==
-[[Category: Campanacci, V.]]
+[[Image:Consurf_key_small.gif|200px|right]]
-[[Category: Gruez, A.]]
+Check<jmol>
-[[Category: Roig-Zamboni, V.]]
+  <jmolCheckbox>
-[[Category: Valencia, C.]]
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pt/1pt5_consurf.spt"</scriptWhenChecked>
-[[Category: ACO]]
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-[[Category: acetylcoa]]
+    <text>to colour the structure by Evolutionary Conservation</text>
-[[Category: coenzyme binding]]
+  </jmolCheckbox>
-[[Category: structural genomics]]
+</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=1pt5 ConSurf].
-[[Category: transferase]]
+<div style="clear:both"></div>
+__TOC__
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:32:17 2008''
+</StructureSection>
+[[Category: Escherichia coli]]
+[[Category: Large Structures]]
+[[Category: Shigella flexneri]]
+[[Category: Cambillau C]]
+[[Category: Campanacci V]]
+[[Category: Gruez A]]
+[[Category: Roig-Zamboni V]]
+[[Category: Valencia C]]