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Structure of d ‐alanine‐ d ‐alanine ligase from Yersinia pestis : nucleotide phosphate recognition by the serine loop
Author(s) -
Tran Huyen-Thi,
Hong Myoung-Ki,
Ngo Ho-Phuong-Thuy,
Huynh Kim-Hung,
Ahn Yeh-Jin,
Wang Zhong,
Kang Lin-Woo
Publication year - 2016
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.374
H-Index - 138
ISSN - 2059-7983
DOI - 10.1107/s2059798315021671
Subject(s) - alanine , dna ligase , peptidoglycan , serine , biochemistry , nucleotide , stereochemistry , chemistry , adenosine triphosphate , amino acid , enzyme , gene
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.