5BPF: Crystal Structure Of Adp Complexed D-alanine-d-alanine Ligase(ddl) From Yersinia Pestis

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 A resolution: apo, AMP-bound, ADP-bound, adenosine 5'-(beta,gamma-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 omega-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 omega-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.
PDB ID: 5BPFDownload
MMDB ID: 136967
PDB Deposition Date: 2015/5/28
Updated in MMDB: 2016/03
Experimental Method:
x-ray diffraction
Resolution: 2.28  Å
Source Organism:
Similar Structures:
Biological Unit for 5BPF: dimeric; determined by author and by software (PISA)
Molecular Components in 5BPF
Label Count Molecule
Proteins (2 molecules)
D-alanine-d-alanine Ligase(Gene symbol: ddl)
Molecule annotation
Chemicals (8 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB