2JI7

X-ray structure of Oxalyl-CoA decarboxylase with covalent reaction intermediate

Summary for 2JI7

• Entry DOI: 10.2210/pdb2ji7/pdb
• Related: 2C31 2JI6 2JI8 2JI9 2JIB
• Descriptor: OXALYL-COA DECARBOXYLASE, 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, MAGNESIUM ION, ... (7 entities in total)
• Functional Keywords: lyase, flavoprotein, decarboxylase, oxalate degradation, intermediate complex, thiamin diphosphate-dependent, thiamine pyrophosphate, non- oxidative decarboxylase
• Biological source: OXALOBACTER FORMIGENES
• Total number of polymer chains: 2
• Total formula weight: 126838.81

Authors

Berthold, C.L.,Toyota, C.G.,Moussatche, P.,Wood, M.D.,Leeper, F.,Richards, N.G.J.,Lindqvist, Y. (deposition date: 2007-02-26, release date: 2007-07-17, Last modification date: 2023-12-13)

Primary citation

Berthold, C.L.,Toyota, C.G.,Moussatche, P.,Wood, M.D.,Leeper, F.,Richards, N.G.J.,Lindqvist, Y.
Crystallographic Snapshots of Oxalyl-Coa Decarboxylase Give Insights Into Catalysis by Nonoxidative Thdp-Dependent Decarboxylases
Structure, 15:853-, 2007

PubMed Abstract: 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.

PubMed: 17637344
DOI: 10.1016/J.STR.2007.06.001

Experimental method

X-RAY DIFFRACTION (1.82 Å)