title: Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop.
abstract: 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.
authors.affiliation: Department of Biological Sciences, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea.
authors.forename: Huyen Thi
authors.initials: HT
authors.lastname: Tran
authors.affiliation: Department of Biological Sciences, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea.
authors.forename: Myoung Ki
authors.initials: MK
authors.lastname: Hong
authors.affiliation: Department of Biological Sciences, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea.
authors.forename: Ho Phuong Thuy
authors.initials: HP
authors.lastname: Ngo
authors.affiliation: Department of Biological Sciences, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea.
authors.forename: Kim Hung
authors.initials: KH
authors.lastname: Huynh
authors.affiliation: Department of Life Science, Sangmyung University, 7 Hongji-dong, Jongno-gu, Seoul 110-743, Republic of Korea.
authors.forename: Yeh Jin
authors.initials: YJ
authors.lastname: Ahn
authors.affiliation: Center for Cellular & Structural Biology, Sun Yat-Sen University, Guangzhou, People's Republic of China.
authors.forename: Zhong
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Department of Biological Sciences, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea.
authors.forename: Lin Woo
authors.initials: LW
authors.lastname: Kang
mesh_terms: D000244:Adenosine Diphosphate / Q000378:metabolism; D000249:Adenosine Monophosphate / Q000378:metabolism; D018360:Crystallography, X-Ray; D004151:Dipeptides / Q000378:metabolism; D062105:Molecular Docking Simulation; D010453:Peptide Synthases / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D015010:Yersinia pestis / Q000737:chemistry / Q000201:enzymology* / Q000378:metabolism
chemical_list: D004151:Dipeptides; C002956:alanylalanine; D000249:Adenosine Monophosphate; D000244:Adenosine Diphosphate; D010453:Peptide Synthases; C019638:D-alanylalanine synthetase
keywords: X-ray crystallography; Yersinia pestis; bacterial cell-wall synthesis; d-alanine-d-alanine ligase; drug targets