4ME6

Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ADP

4ME6 の概要

• エントリーDOI: 10.2210/pdb4me6/pdb
• 関連するPDBエントリー: 3E5N 3R5F 4L1K
• 分子名称: D-alanine--D-alanine ligase, MAGNESIUM ION, ADENOSINE-5'-DIPHOSPHATE, ... (4 entities in total)
• 機能のキーワード: adp-depending enzyme, d-alanine-d-alanine ligase, nucleotide binding, ligase
• 由来する生物種: Xanthomonas oryzae pv. oryzae
• 細胞内の位置: Cytoplasm (By similarity): Q5H614
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 42397.28

構造登録者

Doan, T.T.N.,Kim, J.K.,Ahn, Y.J.,Lee, B.M.,Kang, L.W. (登録日: 2013-08-25, 公開日: 2014-02-19, 最終更新日: 2023-11-08)

主引用文献

Doan, T.N.N.,Kim, J.K.,Ngo, H.P.T.,Tran, H.T.,Cha, S.S.,Chung, K.M.,Huynh, K.H.,Ahn, Y.J.,Kang, L.W.
Crystal structures of d-alanine-d-alanine ligase from Xanthomonas oryzae pv. oryzae alone and in complex with nucleotides
Arch.Biochem.Biophys., 545C:92-99, 2014

PubMed Abstract: 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.

PubMed: 24440607
DOI: 10.1016/j.abb.2014.01.009

実験手法

X-RAY DIFFRACTION (2.1 Å)