Structural basis for phage-mediated activation and repression of bacterial DSR2 anti-phage defense system

Abstract Silent information regulator 2 (Sir2) proteins typically catalyze NAD + -dependent protein deacetylation. The recently identified bacterial Sir2 domain-containing protein, defense-associated sirtuin 2 (DSR2), recognizes the phage tail tube and depletes NAD + to abort phage propagation, which is counteracted by the phage-encoded DSR anti-defense 1 (DSAD1), but their molecular mechanisms remain unclear. Here, we determine cryo-EM structures of inactive DSR2 in its apo form, DSR2–DSAD1 and DSR2–DSAD1–NAD + , as well as active DSR2–tube and DSR2–tube–NAD + complexes. DSR2 forms a tetramer with its C-terminal sensor domains (CTDs) in two distinct conformations: CTD closed or CTD open . Monomeric, rather than oligomeric, tail tube proteins preferentially bind to CTD closed and activate Sir2 for NAD + hydrolysis. DSAD1 binding to CTD open allosterically inhibits tube binding and tube-mediated DSR2 activation. Our findings provide mechanistic insight into DSR2 assembly, tube-mediated DSR2 activation, and DSAD1-mediated inhibition and NAD + substrate catalysis in bacterial DSR2 anti-phage defense systems.