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首页> 外文期刊>Acta crystallographica.Section D. Biological crystallography >Structure of d-alanine-d-alanine ligase from thermus thermophilus HB8: Cumulative conformational change and enzyme-ligand interactions
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Structure of d-alanine-d-alanine ligase from thermus thermophilus HB8: Cumulative conformational change and enzyme-ligand interactions

机译：d-alanine-d-alanine连接酶的结构栖热菌属酸奶HB8:累积构象变化和enzyme-ligand的相互作用

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摘要

d-Alanine-d-alanine ligase (Ddl) is one of the key enzymes in peptidoglycan biosynthesis and is an important target for drug discovery. The enzyme catalyzes the condensation of two d - Ala molecules using ATP to produce d-Ala-d-Ala, which is the terminal peptide of a peptidoglycan monomer. The structures of five forms of the enzyme from Thermus thermophilus HB8 (TtDdl) were determined: unliganded TtDdl (2.3 ? resolution), TtDdl-adenylyl imidodiphosphate (2.6 ?), TtDdl-ADP (2.2 ?), TtDdl-ADP-d-Ala (1.9 ?) and TtDdl-ATP-d-Ala-d-Ala (2.3 ?). The central domain rotates as a rigid body towards the active site in a cumulative manner in concert with the local conformational change of three flexible loops depending upon substrate or product binding, resulting in an overall structural change from the open to the closed form through semi-open and semi-closed forms. Reaction-intermediate models were simulated using TtDdl-complex structures and other Ddl structures previously determined by X-ray methods. The catalytic process accompanied by the cumulative conformational change has been elucidated based on the intermediate models in order to provide new insights regarding the details of the catalytic mechanism.
机译：d-Alanine-d-alanine连接酶(Ddl)是关键之一酶肽聚糖生物合成和是一个药物发现的重要目标。催化两个d -丙氨酸的凝结分子利用ATP生产d-Ala-d-Ala,终端肽的肽聚糖吗单体。酶从栖热菌属酸奶HB8 (TtDdl)决定:unliganded TtDdl(2.3吗?TtDdl-adenylyl imidodiphosphate (2.6 ?)TtDdl-ADP (2.2 ?), TtDdl-ADP-d-Ala(1.9 ?)和TtDdl-ATP-d-Ala-d-Ala(2.3 ?)。旋转刚体对活性部位累积的方式与当地的音乐会构象变化的三个灵活的循环根据底物或产品绑定,导致整体结构变化通过半开的和开放的封闭形式半封闭形式。模拟使用TtDdl-complex结构和以前由其他Ddl结构x射线方法。累积的构象变化阐明基于中间模型对于为了提供新的见解催化机理的细节。

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