7DEQ

Lysozyme-sugar complex in D2O

7DEQ の概要

• エントリーDOI: 10.2210/pdb7deq/pdb
• 分子名称: Lysozyme C, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ... (5 entities in total)
• 機能のキーワード: sugar complex, hydrolase
• 由来する生物種: Gallus gallus (Chicken)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 15326.75

構造登録者

Tanaka, I.,Chatake, T. (登録日: 2020-11-04, 公開日: 2021-03-10, 最終更新日: 2024-11-13)

主引用文献

Tanaka, I.,Nishinomiya, R.,Goto, R.,Shimazaki, S.,Chatake, T.
Recent structural insights into the mechanism of lysozyme hydrolysis.
Acta Crystallogr D Struct Biol, 77:288-292, 2021

PubMed Abstract: Lysozyme hydrolyzes the glycosidic bonds between N-acetylmuramic acid and N-acetylglucosamine in peptidoglycans located in the bacterial cell wall. The mechanism of the hydrolysis reaction of lysozyme was first studied more than 50 years ago; however, it has not yet been fully elucidated and various mechanisms are still being investigated. One reaction system that has commonly been proposed is that the lysozyme intermediate undergoes covalent ligand binding during hydrolysis. However, these findings resulted from experiments performed under laboratory conditions using fluorine-based ligands, which facilitate the formation of covalent bonds between the ligands and the catalytic side chain of lysozyme. More recently, high-resolution X-ray structural analysis was used to study the complex of lysozyme with an N-acetylglucosamine tetramer. As a result, the carboxyl group of Asp52 was found to form a relatively strong hydrogen-bond network and had difficulty binding covalently to C1 of the carbohydrate ring. To confirm this hydrogen-bond network, neutron test measurements were successfully performed to a resolution of better than 1.9 Å.

PubMed: 33645532
DOI: 10.1107/S2059798321000346

実験手法

X-RAY DIFFRACTION (1.03 Å)