Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket

• Published in: Nature (London) 2011-12, Vol.480 (7378), p.565-569
• Main Authors: Nakashima, Ryosuke, Sakurai, Keisuke, Yamasaki, Seiji, Nishino, Kunihiko, Yamaguchi, Akihito
• Format: Article
• Language: English
• Subjects: 631/45/535; 631/92/577; Anthracyclines; Anti-Bacterial Agents - metabolism; Anti-Bacterial Agents - pharmacology; Biological and medical sciences; Chemical properties; Crystalline structure; Erythromycin; Erythromycin - metabolism; Erythromycin - pharmacology; Escherichia coli - drug effects; Escherichia coli - genetics; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - genetics; Fundamental and applied biological sciences. Psychology; Humanities and Social Sciences; letter; Microbial Sensitivity Tests; Models, Molecular; Molecular and cellular biology; Molecular biophysics; Molecules; multidisciplinary; Multidrug Resistance-Associated Proteins - chemistry; Multidrug Resistance-Associated Proteins - genetics; Mutation; Pharmaceutical chemistry; Protein Binding; Protein Structure, Tertiary; Rifampin; Science; Science (multidisciplinary); Structure in molecular biology
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature10641

Crystallographic studies show that high-molecular-mass drugs bind to the bacterial multidrug transporter AcrB at a previously unseen ‘proximal’ binding pocket before peristaltic transfer to the known ‘distal’ pocket, whereas low-molecular-mass drugs bind directly to the distal pocket. Two sites for AcrB drug transporter The crystal structure of the bacterial multidrug efflux transporter AcrB, bound to various antibiotics, has been determined. Rifampicin and erythromycin bind to a previously unseen binding pocket. These high-molecular-weight drugs bind first to the proximal binding pocket and then to the distal pocket after a series of conformational changes. Low-molecular-weight drugs, such as doxorubicin and minocycline, bind directly to the distal binding pocket. AcrB and its homologues are the principal multidrug transporters in Gram-negative bacteria 1 , 2 , 3 , 4 , 5 , 6 and are important in antibiotic drug tolerance 7 , 8 . AcrB is a homotrimer that acts as a tripartite complex 9 , 10 with the outer membrane channel TolC 11 , 12 and the membrane fusion protein AcrA 13 , 14 . Minocycline and doxorubicin have been shown to bind to the phenylalanine cluster region of the binding monomer 15 . Here we report the crystal structures of AcrB bound to the high-molecular-mass drugs rifampicin and erythromycin. These drugs bind to the access monomer, and the binding sites are located in the proximal multisite binding pocket, which is separated from the phenylalanine cluster region (distal pocket) by the Phe-617 loop. Our structures indicate that there are two discrete multisite binding pockets along the intramolecular channel. High-molecular-mass drugs first bind to the proximal pocket in the access state and are then forced into the distal pocket in the binding state by a peristaltic mechanism involving subdomain movements that include a shift of the Phe-617 loop. By contrast, low-molecular-mass drugs, such as minocycline and doxorubicin, travel through the proximal pocket without specific binding and immediately bind to the distal pocket. The presence of two discrete, high-volume multisite binding pockets contributes to the remarkably broad substrate recognition of AcrB.