X-ray Crystallographic Analysis of Xenobiotic Exporter

Proteins of Escherichia coli

Fig. 1. Xenobiotic exporters world. A mammalian cell and a bacterial cell are illustrated.

The xenobiotic exporter proteins, also known asmultidrug efflux transporters, pump a wide variety ofnoxious compounds out of a cell across the cellmembrane. They play an important role in multidrugresistance of pathogenic bacteria and cancer cells[1]. Genomic sequence analysis has revealed thepresence of many putative xenobiotic exporter genesin chromosomes from microorganisms to mammaliancells. There are 19 transporter genes in Es ch er ichi a

c o l i , which actually mediate the efflux of somedrugs and toxic compounds. Among them, AcrB isconstitutively expressed and is a major contributorfor intrinsic drug resistance of E . co li. [2]. AcrBcooperates with a membrane fusion protein, AcrA,and an outer membrane channel, TolC. ThisAcrAB-TolC system exports an unusually widevariety of noxious compounds, e. g. dyes, detergentsand most lipophilic antibiotics directly out of the cell,bypassing the periplasmic space driven by protonmotive force. AcrB is the most important componentof this system; it mediates energy coupling anddetermines substrate specificity (Fig. 1). First of all we cloned a histidine-tagged AcrBinto a multicopy plasmid and overproduced it in

E . coli . Then, AcrB was solubilized and purified inthe presence of a non-ionic detergent, n-dodecyl-β-D-maltopyranoside. Using the vapor diffusionmethod, we obtained crystals of AcrB (space groupR 32), and we employed the multiple isomorphousreplacement method to solve the phase problem. Amolecular model was built and refined at a resolutionof 3.5 Å. All the diffraction data used for structuredetermination were collected at beamline BL44XU(Institute for Protein Research, Osaka Univ.) [3]. AcrB comprises a trimer of 1,049-residueprotomers (Figs. 2(a), 2(b)), and its appearanceresembles that of a jellyfish with a three-foldsymmetry axis perpendicular to the membraneplane. It comprises an extra-membrane (periplasmic)headpiece approximately 50 Å × 100 Å, and atransmembrane region of dimensions 70 Å × 80 Å.The headpiece is divided into two stacked parts:the upper and lower parts are 30-Å and 40-Å thick,respectively. The side view of the upper part has atrapezoidal appearance that is ~ 70-Å wide at thebottom and ~ 40-Å wide at the top. Viewed fromabove, the upper part is open like a funnel, with aninternal diameter of 30 Å. This funnel connected by

cytoplasmic membrane

MDR

drug drug

VMAT

MRP

conjugated drugintracellular vesicles

Mammalian Cell

Bacterial Celldrug

drug

LmrA TetAMacAB Bmr

NorA cytoplasmic membrane

drug

periplasm

outer membraneMexAB-OprM

secondarytransporter

secondarytransporter

ABCtransporter

ATPATP

ATP

ADP+Pi

ADP+Pi

ADP+Pi

AcrAB-TolC

H+

H+

ABCtransporter

H+

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a pore, located between the headpieces of thethree protomers to a large central cavity at theinterface of the headpiece and transmembraneregion of the protomers. Within the membrane, theprotomers are arranged like a ring with a 30-Å holebetween them, which may be filled with phospholipids. The protomers appear to be interlocked by threehairpin-like structures ca . 35 Å long, each protrudingfrom one protomer into the next protomer. Toachieve this mutual insertion, the protomers aretightly packed as a trimer. Between every protomerin the periplasmic domain, there are three vestibulesthat open wide into the periplasm and lead to thecentral cavity inside the headpiece, and a substratelocated in the periplasmic space or on the membraneplane might gain access to the cavity through anyof these vestibules (Fig. 3). The funnel opened atthe top of the AcrB trimer seems to be a perfect fitfor the proximal end of the TolC protein (Fig. 4(a)).The crystal structure of TolC protrudes 100 Å intothe periplasm [4], thus, the sum of the periplasmiclength of AcrB and TolC is ~170 Å, which is justenough to cross the periplasmic space, indicatingthat AcrB and TolC might direct dock with eachother (Fig. 4(a)).

Fig. 2. Structure of AcrB. (a) Side view of a ribbon representation. Three protomers are individuallycoloured. The N-terminal and C-terminal halves of the protomers are depicted by dark and palecolours, respectively. The extra-membrane (periplasmic) headpieces are at the top. (b) Top view of aribbon representation. The protomers are individually colored as in (a).

Fig. 3. A cutaway view displaying thesolvent-accessible surface of AcrB. Thefront protomer is removed. The yellowareas of the surface are colored accordingto residues belonging to the pore helix.

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InnerMembrane

TolC DockingDomains(~30 Å)

PoreDomains(~40 Å)

TransmembraneDomains(~50 Å)

(b)(a)

Fig. 4. (a) Proposed model of the AcrB-AcrA-TolC complex. (b) The schematic mechanism ofxenobioic export mediated by AcrAB-TolC system. The TolC structure dock with the AcrB.

(b)(a)

References[1] Okusu et al. , J. Bacteriol. 178 (1996) 306.[2] Nikaido e t a l., J. Mol. Microb. Biotechnol. 3(2001) 215.[3] Satoshi Murakami, Ryosuke Nakashima, EikiYamashita and Akihito Yamaguchi, Nature 419(2002) 587.[4] V. Koronakis et al. , Nature 405 (2000) 914.

Satoshi Murakamia,b,c , Ryosuke Nakashimaa andAkihito Yamaguchia,c

(a) Osaka University(b) Japan Science and Technology Corporation, PRESTO(c) Japan Science and Technology Corporation, CREST

E-mail: mura@sanken.osaka-u.ac.jp

Xenobiotic substrates from the cytoplasm orinner leaflet of the membrane are transportedthrough every protomer across the membrane andcollect in the central cavity. Substrates from theperiplasmic surface of the inner membrane or theouter leaflet of the membrane also gain access inthe cavity through the vestibules. It appears, then,that substrates in the cavity are actively exportedthrough the pore into the funnel and then on intothe TolC tunnel. The energy for active transport is captured inthe transmembrane region and transmitted to theextra-membrane pore by a remote conformationalcoupling (Fig. 4(b)). This beautiful AcrB structureprovides a great deal of important insight into thefunction of multidrug resistance mediated byxenobiotic exporters. This structure is not only thefirst structure of a multidrug exporter, but also thefirst atomic-level structure of a membrane transporterthat couples with proton translocation across themembrane. Therefore, we believe that this work is

a rea l mi les tone for unders tand ing ac t ivemembrane transport mechanisms based onmolecular structure.

AcrB InnerMembrane

AcrA AcrA

ToIC OuterMembrane

AcrA AcrA

AcrBVestibule Vestibule

Substrate

Substrate Substrate

Substrate

Cytoplasm

CentralCavity

InnerMembrane

Funnel

Pore

ToIC

Periplasm

+H +H

OuterMembrane

MediumSubstrate

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