8ZPH

SFX reaction state structure (40-60min) of alanine racemase

8ZPH の概要

• エントリーDOI: 10.2210/pdb8zph/pdb
• 関連するPDBエントリー: 8ZPE
• 分子名称: Alanine racemase 2, PYRIDOXAL-5'-PHOSPHATE, CHLORIDE ION, ... (5 entities in total)
• 機能のキーワード: enzyme, substrate complex, peptidoglycan synthesis, isomerase
• 由来する生物種: Bacillus subtilis subsp. subtilis str. 168
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 177797.81

構造登録者

Kim, J.,Nam, K.H.,Cho, Y. (登録日: 2024-05-30, 公開日: 2025-01-01, 最終更新日: 2025-01-08)

主引用文献

Kim, J.,Park, J.,Lee, K.,Chung, W.K.,Nam, K.H.,Cho, Y.
Exploring the reaction dynamics of alanine racemase using serial femtosecond crystallography.
Sci Rep, 14:31442-31442, 2024

PubMed Abstract: Alanine racemase (Alr) catalyzes the pyridoxal 5'-phosphate (PLP)-dependent racemization between L- and D-alanine in bacteria. Owing to the potential interest in targeting Alr for antibacterial drug development, several studies have determined the structures of Alr from different species, proposing models for the reaction mechanism. Insights into its reaction dynamics may be conducive to a better understanding of the Alr reaction mechanism. In this study, we determined the structures of the apo and reaction states of Bacillus subtilis Alr (BsAlr) at room temperature using a fixed-target based X-ray free-electron laser. The 2.3 Å resolution structures revealed the alanine substrate or intermediate in various positions at the active site. Conformational change between the N- and C-terminal domains of BsAlr expanded the entryway for substrate binding. In the reaction state of BsAlr, two main alanine binding states were observed: one alanine molecule is positioned away from PLP, whereas the other alanine molecule is covalently bonded to PLP. These structures might represent the dynamic states of the substrate for entrance into, reaction with, or exit from the active site. Our approach provides a simple and rapid method for elucidating the intermediate structure of Alr, which can be expanded to other enzymes.

PubMed: 39733140
DOI: 10.1038/s41598-024-83045-8

実験手法

X-RAY DIFFRACTION (2.3 Å)