SNAP output for PDB entry 8u0u [SNAP web server]

PDB-id

8u0u; SNAP-derived features in text and JSON formats; DNAproDB

Class

immune system-DNA

Method

cryo-EM (3.04 Å)

Summary

Ddmd dimer in complex with ssDNA

Reference

Bravo JPK, Ramos DA, Fregoso Ocampo R, Ingram C, Taylor DW (2024): "Plasmid targeting and destruction by the DdmDE bacterial defence system." Nature, 630, 961-967. doi: 10.1038/s41586-024-07515-9.

Abstract

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.