9BF5

Structure of V. cholerae DdmD in complex with ssDNA

9BF5 の概要

• エントリーDOI: 10.2210/pdb9bf5/pdb
• EMDBエントリー: 44490
• 分子名称: ssDNA1, ssDNA2, Helicase/UvrB N-terminal domain-containing protein (3 entities in total)
• 機能のキーワード: vibrio cholerae, bacteria, anti-plasmid, defense system, dna defense modules(ddm), ddmde, immune system-dna complex, immune system/dna
• 由来する生物種: Vibrio cholerae; 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 280703.13

構造登録者

Shen, Z.F.,Yang, X.Y.,Fu, T.M. (登録日: 2024-04-16, 公開日: 2024-09-04, 最終更新日: 2025-05-28)

主引用文献

Yang, X.Y.,Shen, Z.,Wang, C.,Nakanishi, K.,Fu, T.M.
DdmDE eliminates plasmid invasion by DNA-guided DNA targeting.
Cell, 187:5253-5266.e16, 2024

PubMed Abstract: Horizontal gene transfer is a key driver of bacterial evolution, but it also presents severe risks to bacteria by introducing invasive mobile genetic elements. To counter these threats, bacteria have developed various defense systems, including prokaryotic Argonautes (pAgos) and the DNA defense module DdmDE system. Through biochemical analysis, structural determination, and in vivo plasmid clearance assays, we elucidate the assembly and activation mechanisms of DdmDE, which eliminates small, multicopy plasmids. We demonstrate that DdmE, a pAgo-like protein, acts as a catalytically inactive, DNA-guided, DNA-targeting defense module. In the presence of guide DNA, DdmE targets plasmids and recruits a dimeric DdmD, which contains nuclease and helicase domains. Upon binding to DNA substrates, DdmD transitions from an autoinhibited dimer to an active monomer, which then translocates along and cleaves the plasmids. Together, our findings reveal the intricate mechanisms underlying DdmDE-mediated plasmid clearance, offering fundamental insights into bacterial defense systems against plasmid invasions.

PubMed: 39173632
DOI: 10.1016/j.cell.2024.07.028

実験手法

ELECTRON MICROSCOPY (3.07 Å)