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- Title
Structure of d d-alanine- d d-alanine ligase from Yersinia pestis Yersinia pestis: nucleotide phosphate recognition by the serine loop.
- Authors
Tran, Huyen-Thi; Hong, Myoung-Ki; Ngo, Ho-Phuong-Thuy; Huynh, Kim-Hung; Ahn, Yeh-Jin; Wang, Zhong; Kang, Lin-Woo
- Abstract
d d-Alanyl- d d-alanine is an essential precursor of bacterial peptidoglycan and is synthesized by d 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 from Yersinia pestis 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 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 ω-loop) and loop 4, constitute the binding sites for two d 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 d-alanine and ATP substrates and a substrate-binding mechanism was proposed for YpDDL involving conformational changes of the loops.
- Subjects
ALANINE; BACTERIAL protein structure; YERSINIA pestis
- Publication
Acta Crystallographica: Section D, Structural Biology, 2016, Vol 72, Issue 1, p12
- ISSN
0907-4449
- Publication type
Article
- DOI
10.1107/S2059798315021671