2jib
From Proteopedia
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|PDB= 2jib |SIZE=350|CAPTION= <scene name='initialview01'>2jib</scene>, resolution 2.20Å | |PDB= 2jib |SIZE=350|CAPTION= <scene name='initialview01'>2jib</scene>, resolution 2.20Å | ||
|SITE= <scene name='pdbsite=AC1:Pge+Binding+Site+For+Chain+B'>AC1</scene> | |SITE= <scene name='pdbsite=AC1:Pge+Binding+Site+For+Chain+B'>AC1</scene> | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=ADP:ADENOSINE-5'-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</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> |
| - | |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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2c31|2C31]], [[2ji6|2JI6]], [[2ji7|2JI7]], [[2ji8|2JI8]], [[2ji9|2JI9]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2jib FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jib OCA], [http://www.ebi.ac.uk/pdbsum/2jib PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2jib RCSB]</span> | ||
}} | }} | ||
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[[Category: Toyota, C G.]] | [[Category: Toyota, C G.]] | ||
[[Category: Wood, M D.]] | [[Category: Wood, M D.]] | ||
| - | [[Category: ADP]] | ||
| - | [[Category: COA]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: PGE]] | ||
| - | [[Category: TPP]] | ||
[[Category: decarboxylase]] | [[Category: decarboxylase]] | ||
[[Category: flavoprotein]] | [[Category: flavoprotein]] | ||
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[[Category: thiamine pyrophosphate]] | [[Category: thiamine pyrophosphate]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:58:38 2008'' |
Revision as of 00:58, 31 March 2008
| |||||||
| , resolution 2.20Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | |||||||
| Ligands: | , , , , | ||||||
| Activity: | Oxalyl-CoA decarboxylase, with EC number 4.1.1.8 | ||||||
| Related: | 2C31, 2JI6, 2JI7, 2JI8, 2JI9
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
X-RAY STRUCTURE OF OXALYL-COA DECARBOXYLASE IN COMPLEX WITH COENZYME-A
Overview
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
2JIB is a Single protein structure of sequence from Oxalobacter formigenes. Full crystallographic information is available from OCA.
Reference
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 Mon Mar 31 03:58:38 2008
Categories: Oxalobacter formigenes | Oxalyl-CoA decarboxylase | Single protein | Berthold, C L. | Leeper, F. | Lindqvist, Y. | Moussatche, P. | Richards, N G.J. | Toyota, C G. | Wood, M D. | Decarboxylase | Flavoprotein | Lyase | Non- oxidative decarboxylase | Oxalate degradation | Substrate complex | Thiamin diphosphate-dependent | Thiamine pyrophosphate
