5I8J

Crystal structure of Dmd from phage RB69

5I8J の概要

• エントリーDOI: 10.2210/pdb5i8j/pdb
• 関連するPDBエントリー: 4I8R
• 分子名称: Dmd discriminator of mRNA degradation (2 entities in total)
• 機能のキーワード: antitoxin
• 由来する生物種: Enterobacteria phage RB69
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 14712.81

構造登録者

Wei, Y.,Zhang, H.,Gao, Z.Q.,Dong, Y.H. (登録日: 2016-02-19, 公開日: 2017-02-15, 最終更新日: 2023-11-08)

主引用文献

Wei, Y.,Gao, Z.Q.,Zhang, H.,Dong, Y.H.
Structural characterizations of phage antitoxin Dmd and its interactions with bacterial toxin RnlA
Biochem. Biophys. Res. Commun., 472:592-597, 2016

PubMed Abstract: Toxin-antitoxin (TA) loci are widespread in bacteria plasmids and chromosomes, and target various cellular functions to regulate cell growth and death. A type II TA system RnlA-RnlB from Escherichia coli is associated with phage-resistance. After the infection of bacteriophage T4 with Dmd defection, RnlA is activated by the disappearance of RnlB, resulting in the rapid degradation of T4 mRNAs. Dmd can bind to RnlA directly and neutralize RnlA toxicity to allow phage reproduction. Dmd represent a heterogenous antitoxin of RnlA replacing antitoxin RnlB. Here, we reported two structures of Dmd from T4 phage and RB69 phage. Both Dmd structures are high similar with a compacted domain composed of a four-stranded anti-parallel β-sheet and an α-helix. Chromatography and SAXS suggest Dmd forms a dimer in solution consistent with that in crystal. Structure-based mutagenesis of Dmd reveals key residues involved in RnlA-binding. Possibility cavities in Dmd used for compounds design were modeled. Our structural study revealed the recognition and inhibition mechanism of RnlA by Dmd and providing a potential laboratory phage prevention target for drug design.

PubMed: 26972252
DOI: 10.1016/j.bbrc.2016.03.025

実験手法

X-RAY DIFFRACTION (1.75 Å)