1QPB1QPB の概要
| エントリーDOI | 10.2210/pdb1qpb/pdb |
| 関連するPDBエントリー | 1PVD 1PYD 2VK1 2VK8 2W93 |
| 分子名称 | PYRUVATE DECARBOXYLASE (FORM B), THIAMINE DIPHOSPHATE, MAGNESIUM ION, ... (5 entities in total) |
| 機能のキーワード | thiamine pyruvate, pyruvamide, lyase |
| 由来する生物種 | SACCHAROMYCES PASTORIANUS |
| 細胞内の位置 | Cytoplasm: P06169 |
| タンパク質・核酸の鎖数 | 2 |
| 化学式量合計 | 124183.54 |
| 構造登録者 | |
| 主引用文献 | Lu, G.,Dobritzsch, D.,Baumann, S.,Schneider, G.,Konig, S. The Structural Basis of Substrate Activation in Yeast Pyruvate Decarboxylase a Crystallographic and Kinetic Study Eur.J.Biochem., 267:861-, 2000 Cited by PubMed Abstract: The crystal structure of the complex of the thiamine diphosphate dependent tetrameric enzyme pyruvate decarboxylase (PDC) from brewer's yeast strain with the activator pyruvamide has been determined to 2.4 A resolution. The asymmetric unit of the crystal contains two subunits, and the tetrameric molecule is generated by crystallographic symmetry. Structure analysis revealed conformational nonequivalence of the active sites. One of the two active sites in the asymmetric unit was found in an open conformation, with two active site loop regions (residues 104-113 and 290-304) disordered. In the other subunit, these loop regions are well-ordered and shield the active site from the bulk solution. In the closed enzyme subunit, one molecule of pyruvamide is bound in the active site channel, and is located in the vicinity of the thiazolium ring of the cofactor. A second pyruvamide binding site was found at the interface between the Pyr and the R domains of the subunit in the closed conformation, about 10 A away from residue C221. This second pyruvamide molecule might function in stabilizing the unique orientation of the R domain in this subunit which in turn is important for dimer-dimer interactions in the activated tetramer. No difference electron density in the close vicinity of the side chain of residue C221 was found, indicating that this residue does not form a covalent adduct with an activator molecule. Kinetic experiments showed that substrate activation was not affected by oxidation of cysteine residues and therefore does not seem to be dependent on intact thiol groups in the enzyme. The results suggest that a disorder-order transition of two active-site loop regions is a key event in the activation process triggered by the activator pyruvamide and that covalent modification of C221 is not required for this transition to occur. Based on these findings, a possible mechanism for the activation of PDC by its substrate, pyruvate, is proposed. PubMed: 10651824DOI: 10.1046/J.1432-1327.2000.01070.X 主引用文献が同じPDBエントリー |
| 実験手法 | X-RAY DIFFRACTION (2.4 Å) |
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