A Twist of Fate: The Helix–Turn–Helix Motif in <i>Pseudomonas aeruginosa</i> ExsA Can Allosterically Stabilize the Ligand-Binding Domain

<i>Pseudomonas aeruginosa</i> is an opportunistic human pathogen. One of the most potent virulence factors in its arsenal is the type III secretion system (T3SS). This secretion apparatus injects effector toxins directly into host cells, thereby causing cytotoxicity. The expression of all components of T3SS is regulated by a master transcriptional regulator, ExsA. The inhibition of the latter should therefore lead to the suppression of <i>P. aeruginosa</i> virulence. However, to date, no drugs targeting ExsA have reached the market, and only static structural models of the protein have been generated, focusing on the C-terminal domain (CTD). Here, we used μs atomistic molecular dynamics (MD) simulations to investigate the conformational dynamics of full-length ExsA bound to DNA or DNA free, investigated as monomers or dimers. Our data show how the CTD and NTD of ExsA likely interact with one another and how ExsA binds to DNA. We also analyzed the MD trajectories to predict potential druggable pocket(s) in the structure and relevant geometry. This revealed a lipid-binding pocket within the β-sheet bundle and identified two novel potentially druggable pockets at the NTD/CTD interface, which could be used in future structure-based drug discovery campaigns. Overall, a single helix-turn-helix motif seems to drive DNA recognition in each ExsA monomer and to stabilize the putative ligand-binding domain.