4GP9

Crystal Structure of Benzoylformate Decarboxylase Mutant L403F

Summary for 4GP9

• Entry DOI: 10.2210/pdb4gp9/pdb
• Related: 4GG1 4GM0 4GM1 4GM4 4GPE
• Descriptor: Benzoylformate decarboxylase, CALCIUM ION, 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE, ... (6 entities in total)
• Functional Keywords: decarboxylase, thiamin thiazolone diphosphate cofactor, lyase
• Biological source: Pseudomonas putida
• Total number of polymer chains: 1
• Total formula weight: 58237.57

Authors

Novak, W.R.P.,Andrews, F.H.,Tom, A.R.,Gunderman, P.R.,McLeish, M.J. (deposition date: 2012-08-20, release date: 2013-05-22, Last modification date: 2023-09-13)

Primary citation

Andrews, F.H.,Tom, A.R.,Gunderman, P.R.,Novak, W.R.,McLeish, M.J.
A bulky hydrophobic residue is not required to maintain the v-conformation of enzyme-bound thiamin diphosphate.
Biochemistry, 52:3028-3030, 2013

PubMed Abstract: It is widely accepted that, in thiamin diphosphate (ThDP)-dependent enzymes, much of the rate acceleration is provided by the cofactor. Inter alia, the reactive conformation of ThDP, known as the V-conformation, has been attributed to the presence of a bulky hydrophobic residue located directly below the cofactor. Here we report the use of site-saturation mutagenesis to generate variants of this residue (Leu403) in benzoylformate decarboxylase. The observed 3 orders of magnitude range in k(cat)/K(m) values suggested that conformational changes in the cofactor could be influencing catalysis. However, X-ray structures of several variants were determined, and there was remarkably little change in ThDP conformation. Rather, it seemed that, once the V-conformation was attained, residue size and hydrophobicity were more important for enzyme activity.

PubMed: 23607689
DOI: 10.1021/bi400368j

Experimental method

X-RAY DIFFRACTION (1.07 Å)