Structures of the Mycobacterium tuberculosis efflux pump EfpA reveal the mechanisms of transport and inhibition

• Published in: Nature communications 2024-09, Vol.15 (1), p.7710-11, Article 7710
• Main Authors: Wang, Shuhui, Wang, Kun, Song, Kangkang, Lai, Zon Weng, Li, Pengfei, Li, Dongying, Sun, Yajie, Mei, Ye, Xu, Chen, Liao, Maofu
• Format: Article
• Language: English
• Subjects: 101/28; 101/58; 13/1; 13/106; 13/109; 13/31; 631/326/421; 631/45/612/1237; 631/535/1258/1259; 631/57/2266; 631/57/2283; 82/16; 82/29; 82/80; 82/83; Antitubercular Agents - pharmacology; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Binding Sites; Biological Transport; Cryoelectron Microscopy; Drug delivery; Efflux; Humanities and Social Sciences; Inhibitors; Lipids; Membrane Transport Proteins - chemistry; Membrane Transport Proteins - metabolism; Membranes; Models, Molecular; multidisciplinary; Mycobacterium tuberculosis; Mycobacterium tuberculosis - drug effects; Mycobacterium tuberculosis - metabolism; Protein Conformation; Protein transport; Proteins; Science; Science (multidisciplinary); Structure-function relationships; Therapeutic targets; Tuberculosis
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-51948-9

As the first identified multidrug efflux pump in Mycobacterium tuberculosis ( Mtb ), EfpA is an essential protein and promising drug target. However, the functional and inhibitory mechanisms of EfpA are poorly understood. Here we report cryo-EM structures of EfpA in outward-open conformation, either bound to three endogenous lipids or the inhibitor BRD-8000.3. Three lipids inside EfpA span from the inner leaflet to the outer leaflet of the membrane. BRD-8000.3 occupies one lipid site at the level of inner membrane leaflet, competitively inhibiting lipid binding. EfpA resembles the related lysophospholipid transporter MFSD2A in both overall structure and lipid binding sites and may function as a lipid flippase. Combining AlphaFold-predicted EfpA structure, which is inward-open, we propose a complete conformational transition cycle for EfpA. Together, our results provide a structural and mechanistic foundation to comprehend EfpA function and develop EfpA-targeting anti-TB drugs. Multidrug efflux pump EfpA is an essential protein for M. tuberculosis . The authors determine the structures of Mt EfpA bound to lipids or the inhibitor BRD-8000.3, and propose it may function as a lipid flippase with a defined inhibition mechanism.