2ji8: Difference between revisions
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|PDB= 2ji8 |SIZE=350|CAPTION= <scene name='initialview01'>2ji8</scene>, resolution 2.15Å | |PDB= 2ji8 |SIZE=350|CAPTION= <scene name='initialview01'>2ji8</scene>, resolution 2.15Å | ||
|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= | |LIGAND= <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> | ||
|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]], [[2ji9|2JI9]], [[2jib|2JIB]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ji8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ji8 OCA], [http://www.ebi.ac.uk/pdbsum/2ji8 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2ji8 RCSB]</span> | |||
}} | }} | ||
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[[Category: Toyota, C G.]] | [[Category: Toyota, C G.]] | ||
[[Category: Wood, M D.]] | [[Category: Wood, M D.]] | ||
[[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 03:58:35 2008'' | ||
Revision as of 03:58, 31 March 2008
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| , resolution 2.15Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | |||||||
| Ligands: | , , , , | ||||||
| Activity: | Oxalyl-CoA decarboxylase, with EC number 4.1.1.8 | ||||||
| Related: | 2C31, 2JI6, 2JI7, 2JI9, 2JIB
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| 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
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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)
OCA- Pages with broken file links
- 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
- Product complex
- Thiamin diphosphate-dependent
- Thiamine pyrophosphate