7DRS

Structure of SspE_40224

Summary for 7DRS

• Entry DOI: 10.2210/pdb7drs/pdb
• Descriptor: SspE protein (1 entity in total)
• Functional Keywords: dnase, dna binding protein, gtpase, unknown function, hydrolase
• Biological source: Streptomyces yokosukanensis
• Total number of polymer chains: 4
• Total formula weight: 348589.41

Authors

Haiyan, G.,Jinchuan, Z.,Chen, S.,Wang, L.,Wu, G. (deposition date: 2020-12-29, release date: 2022-06-29, Last modification date: 2023-11-29)

Primary citation

Gao, H.,Gong, X.,Zhou, J.,Zhang, Y.,Duan, J.,Wei, Y.,Chen, L.,Deng, Z.,Wang, J.,Chen, S.,Wu, G.,Wang, L.
Nicking mechanism underlying the DNA phosphorothioate-sensing antiphage defense by SspE.
Nat Commun, 13:6773-6773, 2022

PubMed Abstract: DNA phosphorothioate (PT) modification, with a nonbridging phosphate oxygen substituted by sulfur, represents a widespread epigenetic marker in prokaryotes and provides protection against genetic parasites. In the PT-based defense system Ssp, SspABCD confers a single-stranded PT modification of host DNA in the 5'-CCA-3' motif and SspE impedes phage propagation. SspE relies on PT modification in host DNA to exert antiphage activity. Here, structural and biochemical analyses reveal that SspE is preferentially recruited to PT sites mediated by the joint action of its N-terminal domain (NTD) hydrophobic cavity and C-terminal domain (CTD) DNA binding region. PT recognition enlarges the GTP-binding pocket, thereby increasing GTP hydrolysis activity, which subsequently triggers a conformational switch of SspE from a closed to an open state. The closed-to-open transition promotes the dissociation of SspE from self PT-DNA and turns on the DNA nicking nuclease activity of CTD, enabling SspE to accomplish self-nonself discrimination and limit phage predation, even when only a small fraction of modifiable consensus sequences is PT-protected in a bacterial genome.

PubMed: 36351933
DOI: 10.1038/s41467-022-34505-0

Experimental method

X-RAY DIFFRACTION (3.42 Å)