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.
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.
Department of Biological Sciences, Konkuk University, Seoul, 143-701, Republic of Korea.
Kim-Hung
KH
Huynh
Department of Biological Sciences, Konkuk University, Seoul, 143-701, Republic of Korea.
Myoung-ki
MK
Hong
Department of Biological Sciences, Konkuk University, Seoul, 143-701, Republic of Korea.|The Lawrenceville School, Lawrenceville, NJ, USA.
Clarice
C
Lee
Department of Biological Sciences, Konkuk University, Seoul, 143-701, Republic of Korea.
Huyen-Thi
HT
Tran
National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, 449-728, Republic of Korea.
Sang Hee
SH
Lee
Department of Life Science, Sangmyung University, Seoul, 110-743, Republic of Korea.
Yeh-Jin
YJ
Ahn
Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, Ansan, 426-744, Republic of Korea.
Sun-Shin
SS
Cha
Department of Biological Sciences, Konkuk University, Seoul, 143-701, Republic of Korea. lkang@konkuk.ac.kr.
Lin-Woo
LW
Kang
D040981:Acinetobacter baumannii / Q000201:enzymology* / Q000502:physiology; D055162:Biocatalysis; D018360:Crystallography, X-Ray; D007700:Kinetics; D009711:Nucleotides / Q000502:physiology; D010453:Peptide Synthases / Q000737:chemistry* / Q000378:metabolism; D010457:Peptidoglycan / Q000737:chemistry; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D021122:Protein Subunits
D009711:Nucleotides; D010457:Peptidoglycan; D021122:Protein Subunits; D010453:Peptide Synthases; C019638:D-alanylalanine synthetase
Acinetobacter baumannii; D-alanine-D-alanine ligase; X-ray crystallography; bacterial cell wall synthesis; drug target