2ji8: Difference between revisions

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[[Image:2ji8.png|left|200px]]


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==X-ray structure of Oxalyl-CoA decarboxylase in complex with Formyl- CoA==
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<StructureSection load='2ji8' size='340' side='right'caption='[[2ji8]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
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== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
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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]] 2.15&#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=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>
{{STRUCTURE_2ji8|  PDB=2ji8  |  SCENE=  }}
<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].
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== 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.


===X-RAY STRUCTURE OF OXALYL-COA DECARBOXYLASE IN COMPLEX WITH FORMYL-COA===
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>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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== References ==
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<references/>
{{ABSTRACT_PUBMED_17637344}}
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</StructureSection>
==About this Structure==
[[Category: Large Structures]]
[[2ji8]] is a 2 chain structure with 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=2JI8 OCA].
 
==Reference==
<ref group="xtra">PMID:017637344</ref><references group="xtra"/>
[[Category: Oxalobacter formigenes]]
[[Category: Oxalobacter formigenes]]
[[Category: Oxalyl-CoA decarboxylase]]
[[Category: Berthold CL]]
[[Category: Berthold, C L.]]
[[Category: Leeper F]]
[[Category: Leeper, F.]]
[[Category: Lindqvist Y]]
[[Category: Lindqvist, Y.]]
[[Category: Moussatche P]]
[[Category: Moussatche, P.]]
[[Category: Richards NGJ]]
[[Category: Richards, N G.J.]]
[[Category: Toyota CG]]
[[Category: Toyota, C G.]]
[[Category: Wood MD]]
[[Category: Wood, M D.]]
[[Category: Decarboxylase]]
[[Category: Flavoprotein]]
[[Category: Lyase]]
[[Category: Non- oxidative decarboxylase]]
[[Category: Oxalate degradation]]
[[Category: Product complex]]
[[Category: Thiamin diphosphate-dependent]]
[[Category: Thiamine pyrophosphate]]

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