5DMX

Crystal structure of D-alanine-D-alanine ligase from Acinetobacter baumannii, space group p212121

Summary for 5DMX

• Entry DOI: 10.2210/pdb5dmx/pdb
• Descriptor: D-alanine--D-alanine ligase (2 entities in total)
• Functional Keywords: d-alanine-d-alanine ligase, acinetobacter baumannii, drug target protein, apo structure, ligase
• Biological source: Acinetobacter baumannii ACICU
• Cellular location: Cytoplasm : B2I1J3
• Total number of polymer chains: 6
• Total formula weight: 200356.48

Authors

Huynh, K.H.,Hong, M.K.,Kang, L.W. (deposition date: 2015-09-09, release date: 2016-08-17, Last modification date: 2023-11-08)

Primary citation

Huynh, K.H.,Hong, M.K.,Lee, C.,Tran, H.T.,Lee, S.H.,Ahn, Y.J.,Cha, S.S.,Kang, L.W.
The crystal structure of the D-alanine-D-alanine ligase from Acinetobacter baumannii suggests a flexible conformational change in the central domain before nucleotide binding
J. Microbiol., 53:776-782, 2015

PubMed Abstract: Acinetobacter baumannii, which is emerging as a multidrug-resistant nosocomial pathogen, causes a number of diseases, including pneumonia, bacteremia, meningitis, and skin infections. With ATP hydrolysis, the D-alanine-D-alanine ligase (DDL) catalyzes the synthesis of D-alanyl-D-alanine, which is an essential component of bacterial peptidoglycan. In this study, we determined the crystal structure of DDL from A. baumannii (AbDDL) at a resolution of 2.2 Å. The asymmetric unit contained six protomers of AbDDL. Five protomers had a closed conformation in the central domain, while one protomer had an open conformation in the central domain. The central domain with an open conformation did not interact with crystallographic symmetry-related protomers and the conformational change of the central domain was not due to crystal packing. The central domain of AbDDL can have an ensemble of the open and closed conformations before the binding of substrate ATP. The conformational change of the central domain is important for the catalytic activity and the detail information will be useful for the development of inhibitors against AbDDL and putative antibacterial agents against A. baumannii. The AbDDL structure was compared with that of other DDLs that were in complex with potent inhibitors and the catalytic activity of AbDDL was confirmed using enzyme kinetics assays.

PubMed: 26502962
DOI: 10.1007/s12275-015-5475-8

Experimental method

X-RAY DIFFRACTION (2.81 Å)