8U7B

Crystal structure of Apo form of Short Prokaryotic Argonaute TIR-APAZ (SPARTA) heterodimer

Summary for 8U7B

• Entry DOI: 10.2210/pdb8u7b/pdb
• Descriptor: TIR domain-containing protein, Piwi domain-containing protein, PROLINE, ... (5 entities in total)
• Functional Keywords: sparta, short prokaryotic argonaute, tir, apaz, rna binding protein
• Biological source: Thermoflavifilum thermophilum; More
• Total number of polymer chains: 2
• Total formula weight: 112362.28

Authors

Kottur, J.,Aggarwal, A.K. (deposition date: 2023-09-15, release date: 2024-06-12, Last modification date: 2024-06-19)

Primary citation

Kottur, J.,Malik, R.,Aggarwal, A.K.
Nucleic acid mediated activation of a short prokaryotic Argonaute immune system.
Nat Commun, 15:4852-4852, 2024

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 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.

PubMed: 38844755
DOI: 10.1038/s41467-024-49271-4

Experimental method

X-RAY DIFFRACTION (2.66 Å)