dITP-induced remodeling activates the filamentous effector complex in Kongming anti-phage defense

Several antiviral immune systems based on nucleotide signaling have been identified in bacteria. One of them is the Kongming system, which includes an effector complex (KomBC), composed of a non-canonical purine NTP pyrophosphatase (KomB) and a SIR2 domain-containing protein (KomC). The Kongming system is activated by an atypical signaling nucleotide, dITP, generated upon phage infection. Here, we use structural and functional analyses to show that KomBC assembles into a helical filament, built from vertically stacked 4:4 KomB–KomC repeating units. Binding of dITP to KomB initiates progressive conformational rearrangements within the filament, ultimately remodeling the filament into a distinct architecture in which KomC adopts an active conformation with NADase activity. We further identify a key residue potentially involved in the acquisition of NADase activity in SIR2 family proteins. Thus, our results elucidate the activation mechanism of KomBC, revealing a distinct mode of effector activation by a signaling molecule. Some bacteria use the so-called Kongming immune system, based on nucleotide signaling, to respond to viral infections. Here, the authors show that the Koming effector complex assembles into a helical filament, and the signaling nucleotide induces conformational rearrangements that activate an NADase activity leading to death of infected cells.