8I87

Cryo-EM structure of TIR-APAZ/Ago-gRNA-DNA complex

Summary for 8I87

• Entry DOI: 10.2210/pdb8i87/pdb
• EMDB information: 35240
• Descriptor: TIR domain-containing protein, Piwi domain-containing protein, DNA (5'-D(P*TP*AP*TP*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*A)-3'), ... (5 entities in total)
• Functional Keywords: a protein complex, antiviral protein
• Biological source: Maribacter polysiphoniae; More
• Total number of polymer chains: 16
• Total formula weight: 492958.84

Authors

Zhang, H.,Deng, Z.Q.,Yu, G.M.,Li, X.Z.,Wang, X.S. (deposition date: 2023-02-03, release date: 2023-07-19, Last modification date: 2023-09-13)

Primary citation

Wang, X.,Li, X.,Yu, G.,Zhang, L.,Zhang, C.,Wang, Y.,Liao, F.,Wen, Y.,Yin, H.,Liu, X.,Wei, Y.,Li, Z.,Deng, Z.,Zhang, H.
Structural insights into mechanisms of Argonaute protein-associated NADase activation in bacterial immunity.
Cell Res., 33:699-711, 2023

PubMed Abstract: Nicotinamide adenine dinucleotide (NAD) is a central metabolite in cellular processes. Depletion of NAD has been demonstrated to be a prevalent theme in both prokaryotic and eukaryotic immune responses. Short prokaryotic Argonaute proteins (Agos) are associated with NADase domain-containing proteins (TIR-APAZ or SIR2-APAZ) encoded in the same operon. They confer immunity against mobile genetic elements, such as bacteriophages and plasmids, by inducing NAD depletion upon recognition of target nucleic acids. However, the molecular mechanisms underlying the activation of such prokaryotic NADase/Ago immune systems remain unknown. Here, we report multiple cryo-EM structures of NADase/Ago complexes from two distinct systems (TIR-APAZ/Ago and SIR2-APAZ/Ago). Target DNA binding triggers tetramerization of the TIR-APAZ/Ago complex by a cooperative self-assembly mechanism, while the heterodimeric SIR2-APAZ/Ago complex does not assemble into higher-order oligomers upon target DNA binding. However, the NADase activities of these two systems are unleashed via a similar closed-to-open transition of the catalytic pocket, albeit by different mechanisms. Furthermore, a functionally conserved sensor loop is employed to inspect the guide RNA-target DNA base pairing and facilitate the conformational rearrangement of Ago proteins required for the activation of these two systems. Overall, our study reveals the mechanistic diversity and similarity of Ago protein-associated NADase systems in prokaryotic immune response.

PubMed: 37311833
DOI: 10.1038/s41422-023-00839-7

Experimental method

ELECTRON MICROSCOPY (3.1 Å)