9EZX

Vibrio cholerae DdmD apo complex

Summary for 9EZX

• Entry DOI: 10.2210/pdb9ezx/pdb
• EMDB information: 50090
• Descriptor: Helicase/UvrB N-terminal domain-containing protein (1 entity in total)
• Functional Keywords: helicase, nuclease, complex, effector, immune system
• Biological source: Vibrio cholerae
• Total number of polymer chains: 2
• Total formula weight: 272855.19

Authors

Loeff, L.,Jinek, M. (deposition date: 2024-04-14, release date: 2024-06-19, Last modification date: 2024-07-24)

Primary citation

Loeff, L.,Adams, D.W.,Chanez, C.,Stutzmann, S.,Righi, L.,Blokesch, M.,Jinek, M.
Molecular mechanism of plasmid elimination by the DdmDE defense system.
Science, 385:188-194, 2024

PubMed Abstract: Seventh-pandemic strains contain two pathogenicity islands that encode the DNA defense modules DdmABC and DdmDE. In this study, we used cryogenic electron microscopy to determine the mechanistic basis for plasmid defense by DdmDE. The helicase-nuclease DdmD adopts an autoinhibited dimeric architecture. The prokaryotic Argonaute protein DdmE uses a DNA guide to target plasmid DNA. The structure of the DdmDE complex, validated by in vivo mutational studies, shows that DNA binding by DdmE triggers disassembly of the DdmD dimer and loading of monomeric DdmD onto the nontarget DNA strand. In vitro studies indicate that DdmD translocates in the 5'-to-3' direction, while partially degrading the plasmid DNA. These findings provide critical insights into the mechanism of DdmDE systems in plasmid elimination.

PubMed: 38870273
DOI: 10.1126/science.adq0534

Experimental method

ELECTRON MICROSCOPY (2.55 Å)