Crystal structures of d-alanine-d-alanine ligase from Xanthomonas oryzae pv. oryzae alone and in complex with nucleotides.
D-Alanine-D-alanine ligase (DDL) catalyzes the biosynthesis of d-alanyl-d-alanine, an essential bacterial peptidoglycan precursor, and is an important drug target for the development of antibacterials. We determined four different crystal structures of DDL from Xanthomonas oryzae pv. oryzae (Xoo) causing Bacteria Blight (BB), which include apo, ADP-bound, ATP-bound, and AMPPNP-bound structures at the resolution between 2.3 and 2.0 Å. Similarly with other DDLs, the active site of XoDDL is formed by three loops from three domains at the center of enzyme. Compared with d-alanyl-d-alanine and ATP-bound TtDDL structure, the γ-phosphate of ATP in XoDDL structure was shifted outside toward solution. We swapped the ω-loop (loop3) of XoDDL with those of Escherichia coli and Helicobacter pylori DDLs, and measured the enzymatic kinetics of wild-type XoDDL and two mutant XoDDLs with the swapped ω-loops. Results showed that the direct interactions between ω-loop and other two loops are essential for the active ATP conformation for D-ala-phosphate formation.
Department of Advanced Technology Fusion, Konkuk University, Hwayang dong, Gwangjin-gu, Seoul 143-01, Republic of Korea.
Thanh Thi Ngoc
TT
Doan
Department of Advanced Technology Fusion, Konkuk University, Hwayang dong, Gwangjin-gu, Seoul 143-01, Republic of Korea.
Jin-Kwang
JK
Kim
Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea.
Ho-Phuong-Thuy
HP
Ngo
Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea.
Huyen-Thi
HT
Tran
Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, Ansan 426-744, Republic of Korea.
Sun-Shin
SS
Cha
Department of Microbiology and Immunology, Chonbuk National University Medical School, Jeonju, Jeonbuk 561-756, Republic of Korea.
Kyung
K
Min Chung
Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea.
Kim-Hung
KH
Huynh
Department of Green Life Science, College of Convergence, Sangmyung University, 7 Hongji-dong, Jongno-gu, Seoul 110-743, Republic of Korea.
Yeh-Jin
YJ
Ahn
Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea; Institute for Cellular and Structural Bioloy, Sun Yat-Sen University, Guangzhou, People's Republic of China. Electronic address: lkang@konkuk.ac.kr.
Lin-Woo
LW
Kang
D000255:Adenosine Triphosphate / Q000378:metabolism; D000266:Adenylyl Imidodiphosphate / Q000378:metabolism; D000595:Amino Acid Sequence; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D008969:Molecular Sequence Data; D012275:Oryza / Q000382:microbiology*; D010453:Peptide Synthases / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D016415:Sequence Alignment; D014974:Xanthomonas / Q000737:chemistry / Q000201:enzymology* / Q000378:metabolism
D000266:Adenylyl Imidodiphosphate; D000255:Adenosine Triphosphate; D010453:Peptide Synthases; C019638:D-alanylalanine synthetase
Bacterial cell wall synthesis; Drug target; X-ray crystallography; Xanthomonas oryzae pv. oryzae (Xoo); d-Alanine-d-alanine ligase (DDL)