9JHK

Cryo-EM structure of CpAgo_gDNA-tg_dsDNA monomeric ternary complex

9JHK の概要

• エントリーDOI: 10.2210/pdb9jhk/pdb
• EMDBエントリー: 61485
• 分子名称: Clostridium perfringens Argonaute, DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3'), DNA (29-MER), ... (4 entities in total)
• 機能のキーワード: pagos, nucleotide-binding pocket, paz, cryo-em, dna binding protein/dna, dna binding protein-dna complex
• 由来する生物種: Clostridium perfringens; 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 101693.16

構造登録者

Liu, Y.,Li, S.,Zhang, K. (登録日: 2024-09-10, 公開日: 2025-07-30, 最終更新日: 2026-02-18)

主引用文献

Liu, Y.,Zhang, J.,Liu, J.,Zhang, S.,An, L.,Xie, W.,Zhang, K.,Li, S.
The PAZ pocket and dimerization drive CpAgo's guide-independent and DNA-guided dual catalysis.
Nat Commun, 16:6599-6599, 2025

PubMed Abstract: 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.

PubMed: 40675991
DOI: 10.1038/s41467-025-61926-4

実験手法

ELECTRON MICROSCOPY (3.42 Å)