research papers
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.
Keywords: D-alanine-D-alanine ligase; drug targets; bacterial cell-wall synthesis; Yersinia pestis; X-ray crystallography.
Supporting information
Portable Document Format (PDF) file https://doi.org/10.1107/S2059798315021671/dw5153sup1.pdf |
PDB references: YpDDL, unliganded, 4zqi; complex with ADP, 5bpf; complex with AMP, 5bph; complex with ANP, 5c1o; complex with ADP and D-Ala-D-Ala, 5c1p