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Structure paper

TitleThe PAZ pocket and dimerization drive CpAgo's guide-independent and DNA-guided dual catalysis.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 6599, Year 2025
Publish dateJul 17, 2025
AuthorsYuchan Liu / Jiasu Zhang / Ji Liu / Shengchun Zhang / Linfeng An / Wenbing Xie / Kaiming Zhang / Shanshan Li /
PubMed AbstractArgonaute proteins (Agos) play essential roles in nucleic acid targeting across life domains. While eukaryotic Agos (eAgos) utilize small-interfering RNAs (siRNAs) or microRNAs (miRNAs) for RNA ...Argonaute proteins (Agos) play essential roles in nucleic acid targeting across life domains. While eukaryotic Agos (eAgos) utilize small-interfering RNAs (siRNAs) or microRNAs (miRNAs) for RNA interference, the mechanisms driving prokaryotic Agos (pAgos) in bacterial defense remain underexplored. Here, we characterize the mesophilic pAgo from Clostridium perfringens (CpAgo), which exhibits robust guide-independent and DNA-guided activity at 37 °C. CpAgo efficiently degrades plasmids and structured RNAs into small fragments, generating DNA fragments that serve as guides for subsequent cleavage. Cryo-electron microscopy reveals a positively-charged PAZ nucleotide-binding pocket, critical for both guide-dependent and guide-independent substrate recognition and cleavage. Structural analysis identifies CpAgo's dimerization as a prerequisite for catalytic activity, supporting both nucleic acid degradation and targeted action. Functional assays in Escherichia coli demonstrate CpAgo's role in bacterial defense by mediating plasmid degradation and DNA-guided cleavage. These findings position CpAgo as a critical component of prokaryotic immunity and a promising tool for biotechnology.
External linksNat Commun / PubMed:40675991 / PubMed Central
MethodsEM (single particle)
Resolution2.86 - 3.81 Å
Structure data

61474

9jh7

EMDB-61474, PDB-9jh7:
Cryo-EM structure of CpAgo in complex with the 5'-P guide DNA.
Method: EM (single particle) / Resolution: 3.4 Å

61475

9jh8

EMDB-61475, PDB-9jh8:
Cryo-EM structure of CpAgo_gDNA-tg_ssDNA monomeric ternary complex
Method: EM (single particle) / Resolution: 3.81 Å

61476

9jh9

EMDB-61476, PDB-9jh9:
Cryo-EM structure of CpAgo_gDNA-tg_ssDNA dimeric ternary complex
Method: EM (single particle) / Resolution: 3.42 Å

61485

9jhk

EMDB-61485, PDB-9jhk:
Cryo-EM structure of CpAgo_gDNA-tg_dsDNA monomeric ternary complex
Method: EM (single particle) / Resolution: 3.42 Å

61486

9jhl

EMDB-61486, PDB-9jhl:
Cryo-EM structure of CpAgo_gDNA-tg_dsDNA dimeric ternary complex
Method: EM (single particle) / Resolution: 2.86 Å

61487

9jhm

EMDB-61487, PDB-9jhm:
Cryo-EM structure of CpAgo_gDNA-tg_bubble_dsDNA monomeric ternary complex
Method: EM (single particle) / Resolution: 3.2 Å

61488

9jhn

EMDB-61488, PDB-9jhn:
Cryo-EM structure of CpAgo_gDNA-tg_bubble_dsDNA dimeric ternary complex
Method: EM (single particle) / Resolution: 3.0 Å

Chemicals

ChemComp-MN:
Unknown entry

Source
  • clostridium perfringens (bacteria)
  • synthetic construct (others)
  • clostridium perfringenosum (bacteria)
KeywordsDNA BINDING PROTEIN/DNA / pAgos / nucleotide-binding pocket / PAZ / cryo-EM / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex / dimerization

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