Structure of d-alanine-d-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop

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• 作者：Huyen-Thi Tran ; Myoung-Ki Hong ; Ho-Phuong-Thuy Ngo ; Kim-Hung Huynh ; Yeh-Jin Ahn ; Zhong Wang and Lin-Woo Kang
• 关键词：d-alanine-d-alanine ligase ; drug targets ; bacterial cell-wall synthesis ; Yersinia pestis ; X-ray crystallography
• 刊名：Acta Crystallographica Section D
• 出版年：2016
• 出版时间：January 2016
• 年：2016
• 卷：72
• 期：1
• 页码：12-21
• 全文大小：1755K
• ISSN：1399-0047

文摘

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.