Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket Ryosuke Nakashima, Keisuke Sakurai, Seiji Yamasaki, Kunihiko Nishino & Akihito Yamaguchi http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10641.html Figure 1: Crystal structure of the rifampicin-bound AcrB trimer. http://www.nature.com/nature/journal/vaop/ncurrent/images/nature10641-f1.2.jpg The three AcrB monomers are shown in blue, red and green to indicate the binding, extrusion and access monomers, respectively. This colour scheme is used in all the figures. a, Entire structure of the AcrB trimer with rifampicin viewed from the side and parallel to the membrane plane. The difference Fourier map (Fdrug − Ffree) of bound rifampicin is depicted by an orange mesh, contoured at 4.0σ. b, Cutaway view of the head piece of the AcrB trimer from the distal side of the cell. c, Close-up view of the rifampicin-binding site. Carbon atoms of rifampicin and AcrB are shown in magenta and green, respectively. Nitrogen, oxygen and sulphur atoms are shown in blue, red and yellow, respectively. Hydrogen bonds are indicated by dotted lines. Figure 2: Crystal structure of the erythromycin-binding site of AcrB with a bound erythromycin molecule. http://www.nature.com/nature/journal/vaop/ncurrent/images/nature10641-f2.2.jpg Carbon atoms of erythromycin are shown in yellow. The other colours indicate the same as in Fig. 1c. a, Close-up view of the erythromycin-binding site. Bound erythromycin is shown in yellow, and the difference Fourier map with positive peaks (orange mesh, contoured at 3.0σ) and negative peaks (cyan mesh, contoured at −3.5σ) is shown. b, Overlapping structures of rifampicin and erythromycin at the binding site of AcrB. c, Erythromycin binding site of AcrB with a bound erythromycin molecule. Hydrogen bonds are indicated by dotted lines. Figure 3: Structure of the AcrB trimer with simultaneously bound rifampicin and minocycline. http://www.nature.com/nature/journal/vaop/ncurrent/images/nature10641-f3.2.jpg a, Side view of AcrB with a difference Fourier map of bound rifampicin in the access monomer and minocycline in the binding monomer, which is depicted by a cyan mesh, contoured at 4.0σ. b, Horizontal cutaway view of AcrB. Rifampicin and minocycline are shown in magenta and cyan, respectively, using stick representations, and the Phe-617 loops are shown in red. Figure 4: Effect of site-directed mutagenesis in the two binding pockets and putative intramolecular channels. http://www.nature.com/nature/journal/vaop/ncurrent/images/nature10641-f4.2.jpg a, Close-up view of the erythromycin-binding site with mutated amino-acid residues indicated by blue sticks. The branched intramolecular channels are outlined in black, the Phe-617 loop (Gly 614–Gly 621) is shown in red and bound erythromycin is shown in yellow. For clarity, some residues have been removed from the foreground. b, Growth of mutant-AcrB-expressing E. coli cells in the presence of 32 μg ml−1 erythromycin. c–e, Quenching of doxorubicin fluorescence as a result of doxorubicin accumulation in intact mutant-AcrB-expressing E. coli cells: competitive inhibition of doxorubicin export by various drugs (MINO, minocycline; EM, erythromycin; RF, rifampicin; KM, kanamycin) (c); effect of AcrB mutations on doxorubicin export (d); effect of erythromycin on doxorubicin export by mutant AcrB (e). a.u., arbitrary units. x
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Figure 5: Crystal structure of the rifampicin–minocycline-bound AcrB trimer. http://www.nature.com/nature/journal/vaop/ncurrent/images/nature10641-f5.2.jpg a, Side view of the AcrB trimer with intramolecular channels and bound drugs. The channels are shown as coloured solid surfaces and were calculated using the program CAVER29; the channels include the proximal binding pocket (light green), the distal binding pocket (light pink) and the exit funnel (light yellow). Three channels are labelled, and bound drugs are shown in the CPK representation (rifampicin in magenta and minocycline in cyan). The framework of the central cavity and membrane surface is indicated by solid lines. b, Peristaltic drug transport mechanism of AcrB, with channels labelled as in a. The drugs are transported from a proximal pocket to a distal pocket by peristaltic motion that results from a conformational change from the access state to the binding state.