SNAP output for PDB entry 8squ [SNAP web server]

PDB-id

8squ; SNAP-derived features in text and JSON formats; DNAproDB

Class

immune system

Method

cryo-EM (3.28 Å)

Summary

Monomeric mapsparta bound with guide RNA and target DNA hybrid

Reference

Shen Z, Yang XY, Xia S, Huang W, Taylor DJ, Nakanishi K, Fu TM (2023): "Oligomerization-mediated activation of a short prokaryotic Argonaute." Nature, 621, 154-161. doi: 10.1038/s41586-023-06456-z.

Abstract

While eukaryotic Argonautes and long prokaryotic Argonautes (pAgos) cleave nucleic acids, some short pAgos lack nuclease activity and hydrolyze NAD(P)₊ to induce bacterial cell death₁. We present a hierarchical activation pathway for SPARTA, a short pAgo consisting of an Ago protein and an associated protein TIR-APAZ₂. SPARTA progresses through distinct oligomeric forms, including a monomeric apo state, a monomeric RNA/DNA-bound state, two dimeric RNA/DNA-bound states, and a tetrameric RNA/DNA-bound active state. These snapshots together identify oligomerization as a mechanistic principle of SPARTA activation. Apo SPARTA is inactive, its RNA/DNA-binding channel occupied an auto-inhibitory motif in TIR-APAZ. Upon RNA/DNA binding, SPARTA transitions from a monomer to a symmetric and then an asymmetric dimer, in which two TIR domains interact via charge and shape complementarity. Next, two dimers assemble into a tetramer with a central TIR cluster responsible for hydrolyzing NAD(P)₊. Additionally, we observed unique features of SPARTA-RNA/DNA interactions, including competition between the DNA 3' end and the auto-inhibitory motif, interactions between the RNA G2 nucleotide and Ago, and splaying of the RNA-DNA duplex by two loops exclusive to short pAgos. Together, our findings contribute a mechanistic basis for the activation of short pAgos, a large section of the Ago superfamily.