9BQV image
Entry Detail
PDB ID:
9BQV
EMDB ID:
Keywords:
Title:
DdmD dimer apoprotein
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2024-05-10
Release Date:
2024-07-03
Method Details:
Experimental Method:
Resolution:
3.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Helicase/UvrB N-terminal domain-containing protein
Chain IDs:A, B (auth: F)
Chain Length:1190
Number of Molecules:2
Biological Source:Vibrio cholerae
Ligand Molecules
Primary Citation
Plasmid targeting and destruction by the DdmDE bacterial defence system.
Nature 630 961 967 (2024)
PMID: 38740055 DOI: 10.1038/s41586-024-07515-9

Abstact

Although eukaryotic Argonautes have a pivotal role in post-transcriptional gene regulation through nucleic acid cleavage, some short prokaryotic Argonaute variants (pAgos) rely on auxiliary nuclease factors for efficient foreign DNA degradation1. Here we reveal the activation pathway of the DNA defence module DdmDE system, which rapidly eliminates small, multicopy plasmids from the Vibrio cholerae seventh pandemic strain (7PET)2. Through a combination of cryo-electron microscopy, biochemistry and in vivo plasmid clearance assays, we demonstrate that DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo with a distinctive insertion domain. We observe that the helicase-nuclease DdmD transitions from an autoinhibited, dimeric complex to a monomeric state upon loading of single-stranded DNA targets. Furthermore, the complete structure of the DdmDE-guide-target handover complex provides a comprehensive view into how DNA recognition triggers processive plasmid destruction. Our work establishes a mechanistic foundation for how pAgos utilize ancillary factors to achieve plasmid clearance, and provides insights into anti-plasmid immunity in bacteria.

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Primary Citation of related structures