2ji8: Difference between revisions

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Revision as of 16:26, 23 March 2008

File:2ji8.jpg

, resolution 2.15Å

Sites:

Ligands:

, , , and

Activity:

Oxalyl-CoA decarboxylase, with EC number 4.1.1.8

Coordinates:

save as pdb, mmCIF, xml

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

OverviewOverview

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 StructureAbout this Structure

2JI8 is a Single protein structure of sequence from Oxalobacter formigenes. Full crystallographic information is available from OCA.

ReferenceReference

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

Page seeded by OCA on Sun Mar 23 15:26:41 2008

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OCA

@@ Line 4: / Line 4: @@
 |PDB= 2ji8 |SIZE=350|CAPTION= <scene name='initialview01'>2ji8</scene>, resolution 2.15&Aring;
 |SITE= <scene name='pdbsite=AC1:Pge+Binding+Site+For+Chain+B'>AC1</scene>
-|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene>, <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> and <scene name='pdbligand=PGE:TRIETHYLENE GLYCOL'>PGE</scene>
+|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene>, <scene name='pdbligand=ADP:ADENOSINE-5&#39;-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> and <scene name='pdbligand=PGE:TRIETHYLENE GLYCOL'>PGE</scene>
 |ACTIVITY= [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]
 |GENE=
@@ Line 44: / Line 44: @@
 [[Category: thiamine pyrophosphate]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:42:15 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 15:26:41 2008''