Tran Huyen Thi, Hong Myoung Ki, Ngo Ho Phuong Thuy, Huynh Kim Hung, Ahn Yeh Jin, Wang Zhong, Kang Lin Woo
Department of Biological Sciences, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea.
Department of Life Science, Sangmyung University, 7 Hongji-dong, Jongno-gu, Seoul 110-743, Republic of Korea.
Acta Crystallogr D Struct Biol. 2016 Jan;72(Pt 1):12-21. doi: 10.1107/S2059798315021671. Epub 2016 Jan 1.
D-Alanyl-D-alanine is an essential precursor of bacterial peptidoglycan and is synthesized by D-alanine-D-alanine ligase (DDL) with hydrolysis of ATP; this reaction makes DDL an important drug target for the development of antibacterial agents. Five crystal structures of DDL from Yersinia pestis (YpDDL) were determined at 1.7-2.5 Å resolution: apo, AMP-bound, ADP-bound, adenosine 5'-(β,γ-imido)triphosphate-bound, and D-alanyl-D-alanine- and ADP-bound structures. YpDDL consists of three domains, in which four loops, loop 1, loop 2 (the serine loop), loop 3 (the ω-loop) and loop 4, constitute the binding sites for two D-alanine molecules and one ATP molecule. Some of them, especially the serine loop and the ω-loop, show flexible conformations, and the serine loop is mainly responsible for the conformational change in substrate nucleotide phosphates. Enzyme-kinetics assays were carried out for both the D-alanine and ATP substrates and a substrate-binding mechanism was proposed for YpDDL involving conformational changes of the loops.
D-丙氨酰-D-丙氨酸是细菌肽聚糖的一种必需前体，由D-丙氨酸-D-丙氨酸连接酶（DDL）在ATP水解的情况下合成；该反应使DDL成为开发抗菌剂的重要药物靶点。鼠疫耶尔森菌的DDL（YpDDL）的五个晶体结构在1.7 - 2.5 Å分辨率下被测定：无配体、结合AMP、结合ADP、结合腺苷5'-(β,γ-亚氨基)三磷酸以及结合D-丙氨酰-D-丙氨酸和ADP的结构。YpDDL由三个结构域组成，其中四个环，环1、环2（丝氨酸环）、环3（ω环）和环4，构成两个D-丙氨酸分子和一个ATP分子的结合位点。其中一些环，特别是丝氨酸环和ω环，呈现出灵活的构象，并且丝氨酸环主要负责底物核苷酸磷酸的构象变化。对D-丙氨酸和ATP底物都进行了酶动力学测定，并提出了一种涉及环构象变化的YpDDL底物结合机制。
