1vgr: Difference between revisions

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-[[Image:1vgr.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1vgr", creates the "Structure Box" on the page.
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-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_1vgr|  PDB=1vgr  |  SCENE=  }}
-'''Formyl-CoA transferase mutant Asp169 to Glu'''
+==Formyl-CoA transferase mutant Asp169 to Glu==
+<StructureSection load='1vgr' size='340' side='right'caption='[[1vgr]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1vgr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Oxalobacter_formigenes Oxalobacter formigenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VGR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VGR FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene></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=1vgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vgr OCA], [https://pdbe.org/1vgr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vgr RCSB], [https://www.ebi.ac.uk/pdbsum/1vgr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vgr ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/FCTA_OXAFO FCTA_OXAFO] Catalyzes the transfer of the CoA moiety from formyl-CoA to oxalate. Essential enzyme for the bacterium survival, as it relies on oxalic acid as its sole source of energy.[HAMAP-Rule:MF_00742]
+== 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/vg/1vgr_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=1vgr ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Oxalobacter formigenes is an obligate anaerobe that colonizes the human gastrointestinal tract and employs oxalate breakdown to generate ATP in a novel process involving the interplay of two coupled enzymes and a membrane-bound oxalate:formate antiporter. Formyl-CoA transferase is a critical enzyme in oxalate-dependent ATP synthesis and is the first Class III CoA-transferase for which a high resolution, three-dimensional structure has been determined (Ricagno, S., Jonsson, S., Richards, N., and Lindqvist, Y. (2003) EMBO J. 22, 3210-3219). We now report the first detailed kinetic characterizations of recombinant, wild type formyl-CoA transferase and a number of site-specific mutants, which suggest that catalysis proceeds via a series of anhydride intermediates. Further evidence for this mechanistic proposal is provided by the x-ray crystallographic observation of an acylenzyme intermediate that is formed when formyl-CoA transferase is incubated with oxalyl-CoA. The catalytic mechanism of formyl-CoA transferase is therefore established and is almost certainly employed by all other members of the Class III CoA-transferase family.
-==Overview==
+Kinetic and mechanistic characterization of the formyl-CoA transferase from Oxalobacter formigenes.,Jonsson S, Ricagno S, Lindqvist Y, Richards NG J Biol Chem. 2004 Aug 20;279(34):36003-12. Epub 2004 Jun 21. PMID:15213226<ref>PMID:15213226</ref>
-Oxalobacter formigenes is an obligate anaerobe that colonizes the human gastrointestinal tract and employs oxalate breakdown to generate ATP in a novel process involving the interplay of two coupled enzymes and a membrane-bound oxalate:formate antiporter. Formyl-CoA transferase is a critical enzyme in oxalate-dependent ATP synthesis and is the first Class III CoA-transferase for which a high resolution, three-dimensional structure has been determined (Ricagno, S., Jonsson, S., Richards, N., and Lindqvist, Y. (2003) EMBO J. 22, 3210-3219). We now report the first detailed kinetic characterizations of recombinant, wild type formyl-CoA transferase and a number of site-specific mutants, which suggest that catalysis proceeds via a series of anhydride intermediates. Further evidence for this mechanistic proposal is provided by the x-ray crystallographic observation of an acylenzyme intermediate that is formed when formyl-CoA transferase is incubated with oxalyl-CoA. The catalytic mechanism of formyl-CoA transferase is therefore established and is almost certainly employed by all other members of the Class III CoA-transferase family.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-VGR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Oxalobacter_formigenes Oxalobacter formigenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VGR OCA].
+</div>
+<div class="pdbe-citations 1vgr" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Kinetic and mechanistic characterization of the formyl-CoA transferase from Oxalobacter formigenes., Jonsson S, Ricagno S, Lindqvist Y, Richards NG, J Biol Chem. 2004 Aug 20;279(34):36003-12. Epub 2004 Jun 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15213226 15213226]
+*[[Formyl-CoA transferase|Formyl-CoA transferase]]
-[[Category: Formyl-CoA transferase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Oxalobacter formigenes]]
-[[Category: Single protein]]
+[[Category: Jonsson S]]
-[[Category: Jonsson, S.]]
+[[Category: Lindqvist Y]]
-[[Category: Lindqvist, Y.]]
+[[Category: Ricagno S]]
-[[Category: Ricagno, S.]]
+[[Category: Richards NG]]
-[[Category: Richards, N G.]]
-[[Category: Caib-baif family]]
-[[Category: Coa complex]]
-[[Category: Coa transferase]]
-[[Category: Intertwined]]
-[[Category: Knotted fold]]
-[[Category: Oxalate]]
-[[Category: Oxalate degradation]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 12:31:26 2008''