1KDN

STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE

1KDN の概要

• エントリーDOI: 10.2210/pdb1kdn/pdb
• 分子名称: NUCLEOSIDE DIPHOSPHATE KINASE, MAGNESIUM ION, ALUMINUM FLUORIDE, ... (5 entities in total)
• 機能のキーワード: transferase, kinase, atp-binding, phosphotransferase
• 由来する生物種: Dictyostelium discoideum
• 細胞内の位置: Cytoplasm: P22887
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 52055.46

構造登録者

Cherfils, J.,Xu, Y.W.,Morera, S.,Janin, J. (登録日: 1996-09-10, 公開日: 1997-04-21, 最終更新日: 2024-02-07)

主引用文献

Xu, Y.W.,Morera, S.,Janin, J.,Cherfils, J.
AlF3 mimics the transition state of protein phosphorylation in the crystal structure of nucleoside diphosphate kinase and MgADP.
Proc.Natl.Acad.Sci.USA, 94:3579-3583, 1997

PubMed Abstract: Nucleoside diphosphate kinase reversibly transfers the gamma-phosphate of ATP onto its active site histidine. We have investigated the transition state of histidine phosphorylation with the high-resolution crystal structures of the enzyme from Dictyostelium discoideum with MgADP and either aluminium or beryllium fluoride. The bound aluminium fluoride species is the neutral species AlF3 and not the more common AlF4-. AlF3 forms a trigonal bipyramid that makes it an accurate analog of the transition state of the gamma-phosphate of ATP undergoing transfer to the catalytic histidine. Its axial ligands are a histidine nitrogen and a beta-phosphate oxygen. Beryllium fluoride also binds at the same position and with the same ligands but in a tetrahedral geometry resembling the Michaelis complex rather than the transition state. The two x-ray structures show explicit enzyme-substrate interactions that discriminate between the ground and the transition states of the reaction. They also illustrate the partially dissociative geometry of the transition state of phosphoryl transfer and demonstrate the potential applications of metallofluorides for the study of kinase mechanisms.

PubMed: 9108019
DOI: 10.1073/pnas.94.8.3579

実験手法

X-RAY DIFFRACTION (2 Å)