Structural and enzymatic insights into QatD, a dual-function TatD-like nuclease in the QatABCD anti-phage defense system.

The qatABCD system is a widespread anti-phage module featuring a core QatBC complex, but the specific biological role of its conserved component, QatD, has long been enigmatic. Here, we establish QatD is a TatD-family nuclease co-opted for antiviral defense. The crystal structure of Acinetobacter baumannii QatD reveals a classic TIM-barrel fold featuring a conserved "HxH" active-site motif characteristic of Type II TatD enzymes. Biochemically, QatD exhibits metal-dependent dual activity: a Mg2+-dependent 3'-5' exonuclease and a Ca2+-dependent apurinic/apyrimidinic (AP) endonuclease. We further demonstrate that QatD confers resistance against diverse bacteriophages in vivo, suggesting its defense function is tied to its catalytic activity. Crucially, we discovered that the nuclease activity of QatD is tightly inhibited by physiological concentrations of host nucleoside triphosphates (NTPs). Based on these findings, we propose a mechanistic model wherein the massive nucleotide consumption during rapid viral transcription and replication depletes local host NTP pools, thereby relieving the metabolic inhibition on QatD. The unleashed QatD subsequently targets and degrades single-stranded replication intermediates and AP-site-containing viral genomes. Our work not only elucidates the molecular basis of QatD activation but also highlights an elegant evolutionary strategy wherein bacteria couple metabolic sensing with ancient DNA repair machinery for specialized immune defense.