1p5r: Difference between revisions

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-[[Image:1p5r.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1p5r", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-{{STRUCTURE_1p5r|  PDB=1p5r  |  SCENE=  }}
-'''Formyl-CoA Transferase in complex with Coenzyme A'''
+==Formyl-CoA Transferase in complex with Coenzyme A==
+<StructureSection load='1p5r' size='340' side='right'caption='[[1p5r]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1p5r]] 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=1P5R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P5R 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]] 2.5&#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=1p5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p5r OCA], [https://pdbe.org/1p5r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p5r RCSB], [https://www.ebi.ac.uk/pdbsum/1p5r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p5r 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/p5/1p5r_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=1p5r ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Formyl-CoA transferase catalyses transfer of CoA from formate to oxalate in the first step of oxalate degradation by Oxalobacter formigenes, a bacterium present in the intestinal flora which is implicated in oxalate catabolism in mammals. Formyl-CoA transferase is a member of a family of CoA-transferases for which no structural information is available. We now report the three-dimensional structure of O.formigenes formyl-CoA transferase, which reveals a novel fold and a very striking assembly of the homodimer. The subunit is composed of a large and a small domain where residues from both the N- and C-termini of the subunit are part of the large domain. The linkers between the domains give the subunit a circular shape with a hole in the middle. The enzyme monomers are tightly interacting and are interlocked. This fold requires drastic rearrangement of approximately 75 residues at the C-terminus for formation of the dimer. The structure of a complex of formyl-CoA transferase with CoA is also reported and sets the scene for a mechanistic understanding of enzymes of this family of CoA-transferases.
-==Overview==
+Formyl-CoA transferase encloses the CoA binding site at the interface of an interlocked dimer.,Ricagno S, Jonsson S, Richards N, Lindqvist Y EMBO J. 2003 Jul 1;22(13):3210-9. PMID:12839984<ref>PMID:12839984</ref>
-Formyl-CoA transferase catalyses transfer of CoA from formate to oxalate in the first step of oxalate degradation by Oxalobacter formigenes, a bacterium present in the intestinal flora which is implicated in oxalate catabolism in mammals. Formyl-CoA transferase is a member of a family of CoA-transferases for which no structural information is available. We now report the three-dimensional structure of O.formigenes formyl-CoA transferase, which reveals a novel fold and a very striking assembly of the homodimer. The subunit is composed of a large and a small domain where residues from both the N- and C-termini of the subunit are part of the large domain. The linkers between the domains give the subunit a circular shape with a hole in the middle. The enzyme monomers are tightly interacting and are interlocked. This fold requires drastic rearrangement of approximately 75 residues at the C-terminus for formation of the dimer. The structure of a complex of formyl-CoA transferase with CoA is also reported and sets the scene for a mechanistic understanding of enzymes of this family of CoA-transferases.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-P5R 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=1P5R OCA].
+</div>
+<div class="pdbe-citations 1p5r" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Formyl-CoA transferase encloses the CoA binding site at the interface of an interlocked dimer., Ricagno S, Jonsson S, Richards N, Lindqvist Y, EMBO J. 2003 Jul 1;22(13):3210-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12839984 12839984]
+*[[Formyl-CoA transferase|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 N]]
-[[Category: Richards, N.]]
-[[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 04:43:06 2008''