8K6H

Crystal structure of e.coli cyanase complex with cyanate

8K6H の概要

• エントリーDOI: 10.2210/pdb8k6h/pdb
• 関連するPDBエントリー: 8K6G
• 分子名称: Cyanate hydratase, SULFATE ION, cyanic acid, ... (4 entities in total)
• 機能のキーワード: enzyme, substrate complex, lyase
• 由来する生物種: Escherichia coli K-12
• タンパク質・核酸の鎖数: 10
• 化学式量合計: 177644.49

構造登録者

Kim, J.,Nam, K.H.,Cho, Y. (登録日: 2023-07-25, 公開日: 2023-12-13)

主引用文献

Kim, J.,Kim, Y.,Park, J.,Nam, K.H.,Cho, Y.
Structural mechanism of Escherichia coli cyanase.
Acta Crystallogr D Struct Biol, 79:1094-1108, 2023

PubMed Abstract: Cyanase plays a vital role in the detoxification of cyanate and supplies a continuous nitrogen source for soil microbes by converting cyanate to ammonia and carbon dioxide in a bicarbonate-dependent reaction. The structures of cyanase complexed with dianion inhibitors, in conjunction with biochemical studies, suggest putative binding sites for substrates. However, the substrate-recognition and reaction mechanisms of cyanase remain unclear. Here, crystal structures of cyanase from Escherichia coli were determined in the native form and in complexes with cyanate, bicarbonate and intermediates at 1.5-1.9 Å resolution using synchrotron X-rays and an X-ray free-electron laser. Cyanate and bicarbonate interact with the highly conserved Arg96, Ser122 and Ala123 in the active site. In the presence of a mixture of cyanate and bicarbonate, three different electron densities for intermediates were observed in the cyanase structures. Moreover, the observed electron density could explain the dynamics of the substrate or product. In addition to conformational changes in the substrate-binding pocket, dynamic movement of Leu151 was observed, which functions as a gate for the passage of substrates or products. These findings provide a structural mechanism for the substrate-binding and reaction process of cyanase.

PubMed: 37971797
DOI: 10.1107/S2059798323009609

実験手法

X-RAY DIFFRACTION (1.5 Å)