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.