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TitleA gate-clamp mechanism for ssDNA translocation by DdmD in Vibrio cholerae plasmid defense.
Journal, issue, pagesNucleic Acids Res, Vol. 53, Issue 3, Year 2025
Publish dateJan 24, 2025
AuthorsRuoyu Li / Yusong Liu / Haishan Gao / Zhonghui Lin /
PubMed AbstractThe DdmDE antiplasmid system, consisting of the helicase-nuclease DdmD and the prokaryotic Argonaute (pAgo) protein DdmE, plays a crucial role in defending Vibrio cholerae against plasmids. Guided by ...The DdmDE antiplasmid system, consisting of the helicase-nuclease DdmD and the prokaryotic Argonaute (pAgo) protein DdmE, plays a crucial role in defending Vibrio cholerae against plasmids. Guided by DNA, DdmE specifically targets plasmids, disassembles the DdmD dimer, and forms a DdmD-DdmE handover complex to facilitate plasmid degradation. However, the precise ATP-dependent DNA translocation mechanism of DdmD has remained unclear. Here, we present cryo-EM structures of DdmD bound to single-stranded DNA (ssDNA) in nucleotide-free, ATPγS-bound, and ADP-bound states. These structures, combined with biochemical analysis, reveal a unique "gate-clamp" mechanism for ssDNA translocation by DdmD. Upon ATP binding, arginine finger residues R855 and R858 reorient to interact with the γ-phosphate, triggering HD2 domain movement. This shift repositions the gate residue Q781, causing a flip of the 3' flank base, which is then clamped by residue F639. After ATP hydrolysis, the arginine finger releases the nucleotide, inducing HD2 to return to its open state. This conformational change enables DdmD to translocate along ssDNA by one nucleotide in the 5' to 3' direction. This study provides new insights into the ATP-dependent translocation of DdmD and contributes to understanding the mechanistic diversity within SF2 helicases.
External linksNucleic Acids Res / PubMed:39907109 / PubMed Central
MethodsEM (single particle)
Resolution2.55 - 3.03 Å
Structure data

62357

9khv

EMDB-62357, PDB-9khv:
Structure of DdmD dimer with ssDNA without nucleotide
Method: EM (single particle) / Resolution: 2.55 Å

62360

9khz

EMDB-62360, PDB-9khz:
Structure of DdmD dimer with ssDNA with ADP bound
Method: EM (single particle) / Resolution: 3.03 Å

62361

9ki0

EMDB-62361, PDB-9ki0:
structure of DdmD dimer with ssDNA with AGS
Method: EM (single particle) / Resolution: 2.65 Å

Chemicals

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

Source
  • Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
  • vibrio cholerae o1 biovar el tor str. n16961 (bacteria)
  • synthetic construct (others)
  • vibrio cholerae (bacteria)
KeywordsDNA BINDING PROTEIN/DNA / Helicase/UvrB N-terminal domain-containing protein / DNA BINDING PROTEIN-DNA complex / Helicase/UvrB N-terminal domain-containing protein DdmD

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