SNAP output for PDB entry 7ygh [SNAP web server]

PDB-id

7ygh; SNAP-derived features in text and JSON formats; DNAproDB

Class

hydrolase

Method

X-ray (3.11 Å)

Summary

Crystal structure of the ring nuclease sso2081 from saccharolobus solfataricus in complex with cyclic-tetraadenylate (ca4)

Reference

Du L, Zhang D, Luo Z, Lin Z (2023): "Molecular basis of stepwise cyclic tetra-adenylate cleavage by the type III CRISPR ring nuclease Crn1/Sso2081." Nucleic Acids Res., 51, 2485-2495. doi: 10.1093/nar/gkad101.

Abstract

The cyclic oligoadenylates (cOAs) act as second messengers of the type III CRISPR immunity system through activating the auxiliary nucleases for indiscriminate RNA degradation. The cOA-degrading nucleases (ring nucleases) provide an 'off-switch' regulation of the signaling, thereby preventing cell dormancy or cell death. Here, we describe the crystal structures of the founding member of CRISPR-associated ring nuclease 1 (Crn1) Sso2081 from Saccharolobus solfataricus, alone, bound to phosphate ions or cA4 in both pre-cleavage and cleavage intermediate states. These structures together with biochemical characterizations establish the molecular basis of cA4 recognition and catalysis by Sso2081. The conformational changes in the C-terminal helical insert upon the binding of phosphate ions or cA4 reveal a gate-locking mechanism for ligand binding. The critical residues and motifs identified in this study provide a new insight to distinguish between cOA-degrading and -nondegrading CARF domain-containing proteins.