4DX6: Transport Of Drugs By The Multidrug Transporter Acrb Involves An Access And A Deep Binding Pocket That Are Separated By A Switch-loop

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 A) 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.
PDB ID: 4DX6Download
MMDB ID: 99250
PDB Deposition Date: 2012/2/27
Updated in MMDB: 2012/05
Experimental Method:
x-ray diffraction
Resolution: 2.9  Å
Source Organism:
Escherichia coli K-12
Similar Structures:
Biological Unit for 4DX6: pentameric; determined by author
Molecular Components in 4DX6
Label Count Molecule
Proteins (5 molecules)
Acriflavine Resistance Protein B(Gene symbol: acrB)
Molecule annotation
Molecule annotation
Chemicals (7 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB