Molecular mechanism of toxin neutralization in the HipBST toxin-antitoxin system of Legionella pneumophila

Toxin-antitoxin (TA) systems are ubiquitous genetic modules in bacteria and archaea. Here, we perform structural and biochemical characterization of the Legionella pneumophila effector Lpg2370, demonstrating that it is a Ser/Thr kinase. Together with two upstream genes, lpg2370 constitutes the tripartite HipBST TA. Notably, the toxin Lpg2370 (HipT(Lp)) and the antitoxin Lpg2369 (HipS(Lp)) correspond to the C-terminus and N-terminus of HipA from HipBA TA, respectively. By determining crystal structures of autophosphorylated HipT(Lp), its complex with AMP-PNP, and the structure of HipT(Lp)-HipS(Lp) complex, we identify residues in HipT(Lp) critical for ATP binding and those contributing to its interactions with HipS(Lp). Structural analysis reveals that HipS(Lp) binding induces a loop-to-helix shift in the P-loop of HipT(Lp), leading to the blockage of ATP binding and inhibition of the kinase activity. These findings establish the L. pneumophila effector Lpg2370 as the HipBST TA toxin and elucidate the molecular basis for HipT neutralization in HipBST TA.