2ji8: Difference between revisions

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-[[Image:2ji8.jpg|left|200px]]<br /><applet load="2ji8" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2ji8, resolution 2.15&Aring;" />
-'''X-RAY STRUCTURE OF OXALYL-COA DECARBOXYLASE IN COMPLEX WITH FORMYL-COA'''<br />
-==Overview==
+==X-ray structure of Oxalyl-CoA decarboxylase in complex with Formyl- CoA==
-Despite more than five decades of extensive studies of thiamin diphosphate, (ThDP) enzymes, there remain many uncertainties as to how these enzymes, achieve their rate enhancements. Here, we present a clear picture of, catalysis for the simple nonoxidative decarboxylase, oxalyl-coenzyme A, (CoA) decarboxylase, based on crystallographic snapshots along the, catalytic cycle and kinetic data on active site mutants. First, we provide, crystallographic evidence that, upon binding of oxalyl-CoA, the C-terminal, 13 residues fold over the substrate, aligning the substrate alpha-carbon, for attack by the ThDP-C2 atom. The second structure presented shows a, covalent reaction intermediate after decarboxylation, interpreted as being, nonplanar. Finally, the structure of a product complex is presented. In, accordance with mutagenesis data, no side chains of the enzyme are implied, to directly participate in proton transfer except the glutamic acid, (Glu-56), which promotes formation of the 1',4'-iminopyrimidine tautomer, of ThDP needed for activation.
+<StructureSection load='2ji8' size='340' side='right'caption='[[2ji8]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2ji8]] 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=2JI8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JI8 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]] 2.15&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=FYN:S-{(9R,13S,15R)-17-[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]-9,13,15-TRIHYDROXY-10,10-DIMETHYL-13,15-DIOXIDO-4,8-DIOXO-12,14,16-TRIOXA-3,7-DIAZA-13,15-DIPHOSPHAHEPTADEC-1-YL}+THIOFORMATE'>FYN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</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=2ji8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ji8 OCA], [https://pdbe.org/2ji8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ji8 RCSB], [https://www.ebi.ac.uk/pdbsum/2ji8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ji8 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/OXC_OXAFO OXC_OXAFO]
+== 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/ji/2ji8_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=2ji8 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Despite more than five decades of extensive studies of thiamin diphosphate (ThDP) enzymes, there remain many uncertainties as to how these enzymes achieve their rate enhancements. Here, we present a clear picture of catalysis for the simple nonoxidative decarboxylase, oxalyl-coenzyme A (CoA) decarboxylase, based on crystallographic snapshots along the catalytic cycle and kinetic data on active site mutants. First, we provide crystallographic evidence that, upon binding of oxalyl-CoA, the C-terminal 13 residues fold over the substrate, aligning the substrate alpha-carbon for attack by the ThDP-C2 atom. The second structure presented shows a covalent reaction intermediate after decarboxylation, interpreted as being nonplanar. Finally, the structure of a product complex is presented. In accordance with mutagenesis data, no side chains of the enzyme are implied to directly participate in proton transfer except the glutamic acid (Glu-56), which promotes formation of the 1',4'-iminopyrimidine tautomer of ThDP needed for activation.
-==About this Structure==
+Crystallographic snapshots of oxalyl-CoA decarboxylase give insights into catalysis by nonoxidative ThDP-dependent decarboxylases.,Berthold CL, Toyota CG, Moussatche P, Wood MD, Leeper F, Richards NG, Lindqvist Y Structure. 2007 Jul;15(7):853-61. PMID:17637344<ref>PMID:17637344</ref>
-JI8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Oxalobacter_formigenes Oxalobacter formigenes] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=TPP:'>TPP</scene>, <scene name='pdbligand=ADP:'>ADP</scene>, <scene name='pdbligand=FYN:'>FYN</scene> and <scene name='pdbligand=PGE:'>PGE</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Oxalyl-CoA_decarboxylase Oxalyl-CoA decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.8 4.1.1.8] Known structural/functional Site: <scene name='pdbsite=AC1:Pge+Binding+Site+For+Chain+B'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JI8 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Crystallographic snapshots of oxalyl-CoA decarboxylase give insights into catalysis by nonoxidative ThDP-dependent decarboxylases., Berthold CL, Toyota CG, Moussatche P, Wood MD, Leeper F, Richards NG, Lindqvist Y, Structure. 2007 Jul;15(7):853-61. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17637344 17637344]
+</div>
+<div class="pdbe-citations 2ji8" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Oxalobacter formigenes]]
-[[Category: Oxalyl-CoA decarboxylase]]
+[[Category: Berthold CL]]
-[[Category: Single protein]]
+[[Category: Leeper F]]
-[[Category: Berthold, C.L.]]
+[[Category: Lindqvist Y]]
-[[Category: Leeper, F.]]
+[[Category: Moussatche P]]
-[[Category: Lindqvist, Y.]]
+[[Category: Richards NGJ]]
-[[Category: Moussatche, P.]]
+[[Category: Toyota CG]]
-[[Category: Richards, N.G.J.]]
+[[Category: Wood MD]]
-[[Category: Toyota, C.G.]]
-[[Category: Wood, M.D.]]
-[[Category: ADP]]
-[[Category: FYN]]
-[[Category: MG]]
-[[Category: PGE]]
-[[Category: TPP]]
-[[Category: decarboxylase]]
-[[Category: flavoprotein]]
-[[Category: lyase]]
-[[Category: non- oxidative decarboxylase]]
-[[Category: oxalate degradation]]
-[[Category: product complex]]
-[[Category: thiamin diphosphate-dependent]]
-[[Category: thiamine pyrophosphate]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb  3 10:46:10 2008''