4DX7

Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop

Summary for 4DX7

• Entry DOI: 10.2210/pdb4dx7/pdb
• Related: 4DX5 4DX6
• Descriptor: Acriflavine resistance protein B, DARPIN, DODECYL-BETA-D-MALTOSIDE, ... (10 entities in total)
• Functional Keywords: darpin, multidrug efflux protein, membrane protein, transport protein
• Biological source: Escherichia coli; More
• Cellular location: Cell inner membrane; Multi-pass membrane protein: P31224
• Total number of polymer chains: 5
• Total formula weight: 388258.58

Authors

Eicher, T.,Cha, H.,Seeger, M.A.,Brandstaetter, L.,El-Delik, J.,Bohnert, J.A.,Kern, W.V.,Verrey, F.,Gruetter, M.G.,Diederichs, K.,Pos, K.M. (deposition date: 2012-02-27, release date: 2012-05-02, Last modification date: 2024-02-28)

Primary citation

Eicher, T.,Cha, H.J.,Seeger, M.A.,Brandstatter, L.,El-Delik, J.,Bohnert, J.A.,Kern, W.V.,Verrey, F.,Grutter, M.G.,Diederichs, K.,Pos, K.M.
Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop.
Proc.Natl.Acad.Sci.USA, 109:5687-5692, 2012

PubMed Abstract: AcrAB-TolC is the major efflux protein complex in Escherichia coli extruding a vast variety of antimicrobial agents from the cell. The inner membrane component AcrB is a homotrimer, and it has been postulated that the monomers cycle consecutively through three conformational stages designated loose (L), tight (T), and open (O) in a concerted fashion. Binding of drugs has been shown at a periplasmic deep binding pocket in the T conformation. The initial drug-binding step and transport toward this drug-binding site has been elusive thus far. Here we report high resolution structures (1.9-2.25 Å) of AcrB/designed ankyrin repeat protein (DARPin) complexes with bound minocycline or doxorubicin. In the AcrB/doxorubicin cocrystal structure, binding of three doxorubicin molecules is apparent, with one doxorubicin molecule bound in the deep binding pocket of the T monomer and two doxorubicin molecules in a stacked sandwich arrangement in an access pocket at the lateral periplasmic cleft of the L monomer. This access pocket is separated from the deep binding pocket apparent in the T monomer by a switch-loop. The localization and conformational flexibility of this loop seems to be important for large substrates, because a G616N AcrB variant deficient in macrolide transport exhibits an altered conformation within this loop region. Transport seems to be a stepwise process of initial drug uptake in the access pocket of the L monomer and subsequent accommodation of the drug in the deep binding pocket during the L to T transition to the internal deep binding pocket of the T monomer.

PubMed: 22451937
DOI: 10.1073/pnas.1114944109

Experimental method

X-RAY DIFFRACTION (2.253 Å)