2VK8
Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with its substrate
Summary for 2VK8
| Entry DOI | 10.2210/pdb2vk8/pdb |
| Related | 1PVD 1PYD 1QPB 2VK1 |
| Descriptor | PYRUVATE DECARBOXYLASE ISOZYME 1, THIAMINE DIPHOSPHATE, MAGNESIUM ION, ... (5 entities in total) |
| Functional Keywords | asymmetric active sites, phenylalanine catabolism, tryptophan catabolism, thiamine pyrophosphate, dimer of dimers, phosphorylation, allosteric enzyme, tdp, tpp, lyase, nucleus, pyruvate, cytoplasm, branched-chain amino acid catabolism, substrate activation, thiamine diphosphate, magnesium, acetylation, metal-binding, decarboxylase |
| Biological source | SACCHAROMYCES CEREVISIAE (BAKER'S YEAST) |
| Total number of polymer chains | 4 |
| Total formula weight | 248502.96 |
| Authors | Kutter, S.,Weik, M.,Weiss, M.S.,Konig, S. (deposition date: 2007-12-17, release date: 2009-01-27, Last modification date: 2023-12-13) |
| Primary citation | Kutter, S.,Weiss, M.S.,Wille, G.,Golbik, R.,Spinka, M.,Konig, S. Covalently Bound Substrate at the Regulatory Site of Yeast Pyruvate Decarboxylases Triggers Allosteric Enzyme Activation. J.Biol.Chem., 284:12136-, 2009 Cited by PubMed Abstract: The mechanism by which the enzyme pyruvate decarboxylase from two yeast species is activated allosterically has been elucidated. A total of seven three-dimensional structures of the enzyme, of enzyme variants, or of enzyme complexes from two yeast species, three of them reported here for the first time, provide detailed atomic resolution snapshots along the activation coordinate. The prime event is the covalent binding of the substrate pyruvate to the side chain of cysteine 221, thus forming a thiohemiketal. This reaction causes the shift of a neighboring amino acid, which eventually leads to the rigidification of two otherwise flexible loops, one of which provides two histidine residues necessary to complete the enzymatically competent active site architecture. The structural data are complemented and supported by kinetic investigations and binding studies, providing a consistent picture of the structural changes occurring upon enzyme activation. PubMed: 19246454DOI: 10.1074/JBC.M806228200 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.42 Å) |
Structure validation
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