期刊
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
卷 72, 期 -, 页码 12-21出版社
INT UNION CRYSTALLOGRAPHY
DOI: 10.1107/S2059798315021671
关键词
D-alanine-D-alanine ligase; drug targets; bacterial cell-wall synthesis; Yersinia pestis; X-ray crystallography
资金
- Konkuk University
D-Alanyl-D-alanine is an essential precursor of bacterial peptidoglycan and is synthesized byd d-alanine-d 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 fromYersinia pestis Yersinia pestis (YpDDL) were determined at 1.7-2.5 angstrom resolution: apo, AMP-bound, ADP-bound, adenosine 5-(,-imido)triphosphate-bound, andd d-alanyl-d 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 -loop) and loop 4, constitute the binding sites for twod d-alanine molecules and one ATP molecule. Some of them, especially the serine loop and the -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 thed d-alanine and ATP substrates and a substrate-binding mechanism was proposed for YpDDL involving conformational changes of the loops.
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