Cryo-EM Structure of an Active Bacterial SIR2-STAND Filament

Abstract

The signal transduction ATPases with numerous domains (STAND) superfamily encompasses widely distributed immune systems across bacteria, eukaryotes and archaea. The bacterial antiviral STAND type 5 (Avs5) contains an N-terminal Sirtuin (SIR2) domain, which protects against phage invasion. Despite the established roles of SIR2 and STAND in prokaryotic and eukaryotic immunity, the mechanism underlying their collaboration remains unclear. Here we present cryo-EM structures of Escherichia fergusonii Avs5 (EfAvs5) filaments, elucidating the mechanisms of dimerization, filamentation, filament clustering, ATP binding and NAD+ hydrolysis, all of which are crucial for anti-phage defense. The SIR2 domains and nucleotide-binding oligomerization domains (NOD) engage in the intra- and inter-dimer interaction to form an individual filament, while the outward C-terminal domains contribute to bundle formation. Filamentation potentially stabilizes the dimeric SIR2 configuration, thereby activating the NADase activity of EfAvs5. EfAvs5 is deficient in the ATPase activity, but elevated ATP concentrations can impede its NADase activity. Together, we uncover the filament assembly of Avs5 as a unique mechanism to switch enzyme activities and perform anti-phage defenses.