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==X- | |||
<StructureSection load='2ji7' size='340' side='right' caption='[[2ji7]], [[Resolution|resolution]] 1.82Å' scene=''> | ==X-ray structure of Oxalyl-CoA decarboxylase with covalent reaction intermediate== | ||
<StructureSection load='2ji7' size='340' side='right'caption='[[2ji7]], [[Resolution|resolution]] 1.82Å' scene=''> | |||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2ji7]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[2ji7]] 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=2JI7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JI7 FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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=OXT:3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(1R,11R,15S,17R)-19-[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]-1,11,15,17-TETRAHYDROXY-12,12-DIMETHYL-15,17-DIOXIDO-6,10-DIOXO-14,16,18-TRIOXA-2-THIA-5,9-DIAZA-15,17-DIPHOSPHANONADEC-1-YL}-5-(2-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM'>OXT</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.82Å</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=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=OXT:3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(1R,11R,15S,17R)-19-[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]-1,11,15,17-TETRAHYDROXY-12,12-DIMETHYL-15,17-DIOXIDO-6,10-DIOXO-14,16,18-TRIOXA-2-THIA-5,9-DIAZA-15,17-DIPHOSPHANONADEC-1-YL}-5-(2-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM'>OXT</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr> | |||
<tr | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ji7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ji7 OCA], [https://pdbe.org/2ji7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ji7 RCSB], [https://www.ebi.ac.uk/pdbsum/2ji7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ji7 ProSAT]</span></td></tr> | ||
</table> | |||
<table> | == Function == | ||
[https://www.uniprot.org/uniprot/OXC_OXAFO OXC_OXAFO] | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ji/2ji7_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ji/2ji7_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=2ji7 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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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> | 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 | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 2ji7" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Oxalobacter formigenes]] | [[Category: Oxalobacter formigenes]] | ||
[[Category: Berthold CL]] | |||
[[Category: Berthold | [[Category: Leeper F]] | ||
[[Category: Leeper | [[Category: Lindqvist Y]] | ||
[[Category: Lindqvist | [[Category: Moussatche P]] | ||
[[Category: Moussatche | [[Category: Richards NGJ]] | ||
[[Category: Richards | [[Category: Toyota CG]] | ||
[[Category: Toyota | [[Category: Wood MD]] | ||
[[Category: Wood | |||
Latest revision as of 17:49, 13 December 2023
X-ray structure of Oxalyl-CoA decarboxylase with covalent reaction intermediateX-ray structure of Oxalyl-CoA decarboxylase with covalent reaction intermediate
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedDespite 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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