5C1O

Crystal structure of AMP-PNP complexed D-alanine-D-alanine ligase(DDL) from Yersinia pestis

5C1O の概要

• エントリーDOI: 10.2210/pdb5c1o/pdb
• 関連するPDBエントリー: 5C1P
• 分子名称: D-alanine--D-alanine ligase, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, SODIUM ION, ... (5 entities in total)
• 機能のキーワード: d-alanine-d-alanine ligase, ddl, drug target, bacterial cell wall synthesis, ligase
• 由来する生物種: Yersinia pestis
• 細胞内の位置: Cytoplasm : Q8ZIE7
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 134956.11

構造登録者

Tran, H.T.,Kang, L.W.,Hong, M.K. (登録日: 2015-06-15, 公開日: 2016-03-02, 最終更新日: 2024-03-20)

主引用文献

Tran, H.T.,Hong, M.K.,Ngo, H.P.,Huynh, K.H.,Ahn, Y.J.,Wang, Z.,Kang, L.W.
Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop.
Acta Crystallogr D Struct Biol, 72:12-21, 2016

PubMed 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.

PubMed: 26894530
DOI: 10.1107/S2059798315021671

実験手法

X-RAY DIFFRACTION (2.5 Å)