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Title | Nucleic acid mediated activation of a short prokaryotic Argonaute immune system. |
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Journal, issue, pages | Nat Commun, Vol. 15, Issue 1, Page 4852, Year 2024 |
Publish date | Jun 6, 2024 |
Authors | Jithesh Kottur / Radhika Malik / Aneel K Aggarwal / |
PubMed Abstract | A short prokaryotic Argonaute (pAgo) TIR-APAZ (SPARTA) defense system, activated by invading DNA to unleash its TIR domain for NAD(P) hydrolysis, was recently identified in bacteria. We report the ...A short prokaryotic Argonaute (pAgo) TIR-APAZ (SPARTA) defense system, activated by invading DNA to unleash its TIR domain for NAD(P) hydrolysis, was recently identified in bacteria. We report the crystal structure of SPARTA heterodimer in the absence of guide-RNA/target-ssDNA (2.66 Å) and a cryo-EM structure of the SPARTA oligomer (tetramer of heterodimers) bound to guide-RNA/target-ssDNA at nominal 3.15-3.35 Å resolution. The crystal structure provides a high-resolution view of SPARTA, revealing the APAZ domain as equivalent to the N, L1, and L2 regions of long pAgos and the MID domain containing a unique insertion (insert57). Cryo-EM structure reveals regions of the PIWI (loop10-9) and APAZ (helix αN) domains that reconfigure for nucleic-acid binding and decrypts regions/residues that reorganize to expose a positively charged pocket for higher-order assembly. The TIR domains amass in a parallel-strands arrangement for catalysis. We visualize SPARTA before and after RNA/ssDNA binding and uncover the basis of its active assembly leading to abortive infection. |
External links | Nat Commun / PubMed:38844755 / PubMed Central |
Methods | EM (single particle) / X-ray diffraction |
Resolution | 2.66 - 3.37 Å |
Structure data | EMDB-41945: Locally refined (symmetry based) cryo-EM map of the dimer of the SPARTA oligomer with guide RNA and target DNA EMDB-41947: Locally refined (symmetry based) cryo-EM map of the second dimer of the SPARTA oligomer with guide RNA and target DNA EMDB-41948: Focused refined cryo-EM map of the TIR domains of the SPARTA oligomer EMDB-41959: Original Cryo-EM map of the SPARTA oligomer with guide RNA and target DNA EMDB-41966, PDB-8u72: PDB-8u7b: |
Chemicals | ChemComp-MG: ChemComp-HOH: ChemComp-PRO: ChemComp-MN: |
Source |
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Keywords | RNA BINDING PROTEIN/RNA/DNA / RNA / DNA / Argonaute / TIR / immune system / RNA BINDING PROTEIN-RNA-DNA complex / RNA BINDING PROTEIN / SPARTA / Short Prokaryotic Argonaute / APAZ |