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2ji9

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{{Seed}}
 
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[[Image:2ji9.png|left|200px]]
 
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==X-ray structure of Oxalyl-CoA decarboxylase in complex with 3-deaza- ThDP==
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The line below this paragraph, containing "STRUCTURE_2ji9", creates the "Structure Box" on the page.
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<StructureSection load='2ji9' size='340' side='right'caption='[[2ji9]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2ji9]] 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=2JI9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JI9 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
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<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=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPW:2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL+TRIHYDROGEN+DIPHOSPHATE'>TPW</scene></td></tr>
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{{STRUCTURE_2ji9| PDB=2ji9 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ji9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ji9 OCA], [https://pdbe.org/2ji9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ji9 RCSB], [https://www.ebi.ac.uk/pdbsum/2ji9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ji9 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/OXC_OXAFO OXC_OXAFO]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ji/2ji9_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2ji9 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===X-RAY STRUCTURE OF OXALYL-COA DECARBOXYLASE IN COMPLEX WITH 3-DEAZA-THDP===
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_17637344}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2ji9" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 17637344 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_17637344}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2JI9 is a 2 chains structure of sequences 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=2JI9 OCA].
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==Reference==
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<ref group="xtra">PMID:17637344</ref><references group="xtra"/>
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[[Category: Oxalobacter formigenes]]
[[Category: Oxalobacter formigenes]]
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[[Category: Oxalyl-CoA decarboxylase]]
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[[Category: Berthold CL]]
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[[Category: Berthold, C L.]]
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[[Category: Leeper F]]
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[[Category: Leeper, F.]]
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[[Category: Lindqvist Y]]
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[[Category: Lindqvist, Y.]]
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[[Category: Moussatche P]]
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[[Category: Moussatche, P.]]
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[[Category: Richards NGJ]]
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[[Category: Richards, N G.J.]]
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[[Category: Toyota CG]]
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[[Category: Toyota, C G.]]
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[[Category: Wood MD]]
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[[Category: Wood, M D.]]
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[[Category: Cofactor analogue inhibitor complex]]
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[[Category: Decarboxylase]]
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[[Category: Flavoprotein]]
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[[Category: Lyase]]
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[[Category: Non- oxidative decarboxylase]]
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[[Category: Oxalate degradation]]
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[[Category: Thiamin diphosphate-dependent]]
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[[Category: Thiamine pyrophosphate]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:59:54 2009''
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Current revision

X-ray structure of Oxalyl-CoA decarboxylase in complex with 3-deaza- ThDP

PDB ID 2ji9

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