5BPH

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

Summary for 5BPH

• Entry DOI: 10.2210/pdb5bph/pdb
• Related: 5BPF
• Descriptor: D-alanine--D-alanine ligase, ADENOSINE MONOPHOSPHATE, SODIUM ION, ... (6 entities in total)
• Functional Keywords: d-alanine-d-alanine ligase (ddl), drug target; bacterial cell wall synthesis, ligase
• Biological source: Yersinia pestis
• Cellular location: Cytoplasm : Q8ZIE7
• Total number of polymer chains: 4
• Total formula weight: 135221.91

Authors

Tran, H.T.,Kang, L.W.,Hong, M.K. (deposition date: 2015-05-28, release date: 2016-03-02, Last modification date: 2024-03-20)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.7 Å)