Structural Superimposition

Abstact

The growing crisis of antimicrobial resistance demands urgent need for antibiotics with alternative targets and modes of action (MOAs). Lipoproteins play crucial roles in bacterial survival and immunoregulation. The lipoprotein transporter, known as LolCDE or LolDF, has recently emerged as an effective target for selectively killing pathogenic bacteria such as Acinetobacter baumannii while sparing gut microbiota. While the heterodimeric LolCDE in Escherichia coli has been extensively studied, the druggable pocket and structural dynamics of the distinct homodimeric LolDF that exists in many critical pathogens are poorly understood. Such a knowledge gap limits our ability to exploit the Lol system to develop drugs with desired spectra of antibacterial activity. Here we determine the cryo-EM structures of homodimeric LolDF of A. baumannii in nucleotide-free apo-closed, vanadate-trapped fully closed, and inhibitor-bound open conformations, revealing the distinct structural features and conformational cycle of LolDF. Further cryo-EM, biochemical and functional analyses uncover the MOA of abaucin, a recently identified LolDF-targeting compound, demonstrating how multiple abaucin molecules open LolDF in a stepwise manner to establish an induced-fit pocket. Together, our results advance the understanding of LolDF function and inhibition, and provide the cryptic druggable conformation and specific inhibitor-bound pocket for structure-based drug discovery to target the dynamic lipoprotein transporter in A. baumannii.