Crystal structures of d-alanine-d-alanine ligase from Xanthomonas oryzae pv. oryzae alone and in complex with nucleotides

Thanh Thi Ngoc Doan, Jin Kwang Kim, Ho Phuong Thuy Ngo, Huyen Thi Tran, Sun Shin Cha, Kyung Min Chung, Kim Hung Huynh, Yeh Jin Ahn, Lin Woo Kang

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11 Scopus citations


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.

Original languageEnglish
Pages (from-to)92-99
Number of pages8
JournalArchives of Biochemistry and Biophysics
StatePublished - 1 Mar 2014

Bibliographical note

Funding Information:
We are grateful to Dr. Kunio Hirata at beamline XU32 in RIKEN/SPring-8 center, JAPAN, and the staff members at beamline 17A in KEK/Photon factory for their assistance, respectively. This work was supported by Grants from the Next-Generation BioGreen 21 Program (No. PJ009082 ), the Rural Development Administration, Republic of Korea, the Korean National Research Foundation (NRF) (NRF-2012R1A2A2A02005978), and the Introduced Innovative R&D Team Leadership of Guangdong Province, People's Republic of China. Appendix A


  • Bacterial cell wall synthesis
  • Drug target
  • X-ray crystallography
  • Xanthomonas oryzae pv. oryzae (Xoo)
  • d-Alanine-d-alanine ligase (DDL)


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