PDBsum entry 2hrt

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Membrane protein, transport protein PDB id
Protein chains
(+ 0 more) 1032 a.a. *
FLC ×4
* Residue conservation analysis
PDB id:
Name: Membrane protein, transport protein
Title: Asymmetric structure of trimeric acrb from escherichia coli
Structure: Acriflavine resistance protein b. Chain: a, b, c, d, e, f. Engineered: yes
Source: Escherichia coli k12. Organism_taxid: 83333. Strain: k-12. Gene: acrb, acre. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
3.00Å     R-factor:   0.234     R-free:   0.274
Authors: M.A.Seeger,A.Schiefner,T.Eicher,F.Verrey,K.Diederichs,K.M.Po
Key ref:
M.A.Seeger et al. (2006). Structural asymmetry of AcrB trimer suggests a peristaltic pump mechanism. Science, 313, 1295-1298. PubMed id: 16946072 DOI: 10.1126/science.1131542
20-Jul-06     Release date:   12-Sep-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P31224  (ACRB_ECOLI) -  Multidrug efflux pump subunit AcrB
1049 a.a.
1032 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   4 terms 
  Biological process     transport   4 terms 
  Biochemical function     transporter activity     4 terms  


DOI no: 10.1126/science.1131542 Science 313:1295-1298 (2006)
PubMed id: 16946072  
Structural asymmetry of AcrB trimer suggests a peristaltic pump mechanism.
M.A.Seeger, A.Schiefner, T.Eicher, F.Verrey, K.Diederichs, K.M.Pos.
The AcrA/AcrB/TolC complex spans the inner and outer membranes of Escherichia coli and serves as its major drug-resistance pump. Driven by the proton motive force, it mediates the efflux of bile salts, detergents, organic solvents, and many structurally unrelated antibiotics. Here, we report a crystallographic structure of trimeric AcrB determined at 2.9 and 3.0 angstrom resolution in space groups that allow asymmetry of the monomers. This structure reveals three different monomer conformations representing consecutive states in a transport cycle. The structural data imply an alternating access mechanism and a novel peristaltic mode of drug transport by this type of transporter.
  Selected figure(s)  
Figure 1.
Fig. 1. Main structural differences of the AcrB monomers. (A) The three AcrB monomers shown in top view as cylinder presentation in blue (L), yellow (T), and red (O) are superimposed onto the symmetric AcrB trimer model depicted in transparent gray. In the T monomer (yellow), a hydrophobic pocket is defined by phenylalanines 136, 178, 610, 615, 617, and 628; valines 139 and 612; isoleucines 277 and 626; and tyrosine 327 at the PN2/PC1 interface. (B) Structural changes in the putative proton translocation site. Conserved residues D407, D408 (TM4), and K940 (TM10) in the three monomers (L, blue; T, yellow; O, red) are depicted with 2Fo-Fc electron density maps contoured at 0.5 (L) or 1 (T and O) as viewed from the cytoplasm. In the L and T monomers, the same conformation is observed, whereas in the O monomer, K940 forms a salt bridge with D407. This interaction seems to be stabilized by hydrogen bonding of T978 (TM11). To restore the geometry as it appears in the L monomer, proton uptake is anticipated.
Figure 3.
Fig. 3. Schematic representation of the AcrB alternating site functional rotation transport mechanism. The conformational states loose (L), tight (T), and open (O) are colored blue, yellow and red, respectively. (A) Side-view schematic representation of two of the three monomers of the AcrB trimer. AcrA and TolC are indicated in light green and light purple colors, respectively. The proposed proton translocation site (D407, D408, and K940) is indicated in the membrane part of each monomer. (B) The lateral grooves in the L and T monomer indicate the substrate binding sites. The different geometric forms reflect low (triangle), high (rectangle), or no (circle) binding affinity for the transported substrates. The PN1 subdomains (including the pore helices) located in the middle of the model are highlighted and form the corners of an asymmetric triangle (white) to indicate the communication between the monomers. In the first state of the cycle, a monomer binds a substrate (acridine) in its transmembrane domain (L conformation), subsequently transports the substrate from the transmembrane domain to the hydrophobic binding pocket (conversion to T conformation) and finally releases the substrate in the funnel toward TolC (O conformation). The conversion from the O-monomer to the L-monomer conformation is suggested to be the major energy-requiring (proton motive force–dependent) step in this functional rotation cycle and requires the binding of a proton to the proton translocation site (D407, D408, and K940) from the periplasm. The conversion from the T monomer to the O monomer is accompanied by the release of a proton from the proton translocation site to the cytoplasm. AcrA can be expected to participate in the transduction of the conformational changes from AcrB to TolC, which results in the opening of the TolC channel and the facilitation of drug extrusion to the outside of the cell.
  The above figures are reprinted by permission from the AAAs: Science (2006, 313, 1295-1298) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20981744 C.C.Su, F.Long, and E.W.Yu (2011).
The Cus efflux system removes toxic ions via a methionine shuttle.
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Crystal structure of the CusBA heavy-metal efflux complex of Escherichia coli.
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PDB code: 3ne5
21112401 C.Ebel (2011).
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21513873 C.Oswald, and K.M.Pos (2011).
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21513882 E.B.Tikhonova, Y.Yamada, and H.I.Zgurskaya (2011).
Sequential mechanism of assembly of multidrug efflux pump AcrAB-TolC.
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A single acidic residue can guide binding site selection but does not govern QacR cationic-drug affinity.
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PDB code: 3pm1
21296164 N.Monroe, G.Sennhauser, M.A.Seeger, C.Briand, and M.G.Grütter (2011).
Designed ankyrin repeat protein binders for the crystallization of AcrB: Plasticity of the dominant interface.
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PDB codes: 3noc 3nog
22121023 R.Nakashima, K.Sakurai, S.Yamasaki, K.Nishino, and A.Yamaguchi (2011).
Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket.
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PDB codes: 3aoa 3aob 3aoc 3aod
21115481 T.K.Janganan, L.Zhang, V.N.Bavro, D.Matak-Vinkovic, N.P.Barrera, M.F.Burton, P.G.Steel, C.V.Robinson, M.I.Borges-Walmsley, and A.R.Walmsley (2011).
Opening of the outer membrane protein channel in tripartite efflux pumps is induced by interaction with the membrane fusion partner.
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21245342 X.Y.Pei, P.Hinchliffe, M.F.Symmons, E.Koronakis, R.Benz, C.Hughes, and V.Koronakis (2011).
Structures of sequential open states in a symmetrical opening transition of the TolC exit duct.
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PDB codes: 2wmz 2xmn
20583998 A.Welch, C.U.Awah, S.Jing, H.W.van Veen, and H.Venter (2010).
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Chaperone-mediated copper handling in the periplasm.
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Metal-induced conformational changes in ZneB suggest an active role of membrane fusion proteins in efflux resistance systems.
  Proc Natl Acad Sci U S A, 107, 11038-11043.
PDB code: 3lnn
20804453 F.Husain, and H.Nikaido (2010).
Substrate path in the AcrB multidrug efflux pump of Escherichia coli.
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20865003 F.Long, C.C.Su, M.T.Zimmermann, S.E.Boyken, K.R.Rajashankar, R.L.Jernigan, and E.W.Yu (2010).
Crystal structures of the CusA efflux pump suggest methionine-mediated metal transport.
  Nature, 467, 484-488.
PDB codes: 3k07 3kso 3kss
20399187 G.Phan, H.Benabdelhak, M.B.Lascombe, P.Benas, S.Rety, M.Picard, A.Ducruix, C.Etchebest, and I.Broutin (2010).
Structural and dynamical insights into the opening mechanism of P. aeruginosa OprM channel.
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PDB code: 3d5k
20038594 H.S.Kim, D.Nagore, and H.Nikaido (2010).
Multidrug efflux pump MdtBC of Escherichia coli is active only as a B2C heterotrimer.
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20606071 J.A.Bohnert, B.Karamian, and H.Nikaido (2010).
Optimized Nile Red efflux assay of AcrAB-TolC multidrug efflux system shows competition between substrates.
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20132445 J.W.Weeks, T.Celaya-Kolb, S.Pecora, and R.Misra (2010).
AcrA suppressor alterations reverse the drug hypersensitivity phenotype of a TolC mutant by inducing TolC aperture opening.
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19826804 K.McLuskey, A.W.Roszak, Y.Zhu, and N.W.Isaacs (2010).
Crystal structures of all-alpha type membrane proteins.
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20667175 K.R.Vinothkumar, and R.Henderson (2010).
Structures of membrane proteins.
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19961541 R.Ernst, P.Kueppers, J.Stindt, K.Kuchler, and L.Schmitt (2010).
Multidrug efflux pumps: substrate selection in ATP-binding cassette multidrug efflux pumps--first come, first served?
  FEBS J, 277, 540-549.  
20548943 R.Schulz, A.V.Vargiu, F.Collu, U.Kleinekathöfer, and P.Ruggerone (2010).
Functional rotation of the transporter AcrB: insights into drug extrusion from simulations.
  PLoS Comput Biol, 6, e1000806.  
20160052 S.P.Lim, and H.Nikaido (2010).
Kinetic parameters of efflux of penicillins by the multidrug efflux transporter AcrAB-TolC of Escherichia coli.
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20145935 W.Behrens-Baumann, U.Frank, and T.Ness (2010).
[Rational antibiotic therapy in ophthalmology].
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Drug export and allosteric coupling in a multidrug transporter revealed by molecular simulations.
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20212112 Y.Takatsuka, C.Chen, and H.Nikaido (2010).
Mechanism of recognition of compounds of diverse structures by the multidrug efflux pump AcrB of Escherichia coli.
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20676995 Y.Takatsuka, and H.Nikaido (2010).
Site-directed disulfide cross-linking to probe conformational changes of a transporter during its functional cycle: Escherichia coli AcrB multidrug exporter as an example.
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19695261 C.C.Su, F.Yang, F.Long, D.Reyon, M.D.Routh, D.W.Kuo, A.K.Mokhtari, J.D.Van Ornam, K.L.Rabe, J.A.Hoy, Y.J.Lee, K.R.Rajashankar, and E.W.Yu (2009).
Crystal structure of the membrane fusion protein CusB from Escherichia coli.
  J Mol Biol, 393, 342-355.
PDB codes: 3h94 3h9i 3h9t 3ooc 3opo 3ow7
18936189 C.Wehmeier, S.Schuster, E.Fähnrich, W.V.Kern, and J.A.Bohnert (2009).
Site-directed mutagenesis reveals amino acid residues in the Escherichia coli RND efflux pump AcrB that confer macrolide resistance.
  Antimicrob Agents Chemother, 53, 329-330.  
19219012 E.Schleiff, and R.Tampé (2009).
Membrane proteins take center stage in Frankfurt.
  Nat Chem Biol, 5, 135-139.  
19136595 H.I.Zgurskaya (2009).
Covalently linked AcrB giant offers a new powerful tool for mechanistic analysis of multidrug efflux in bacteria.
  J Bacteriol, 191, 1727-1728.  
19722844 H.I.Zgurskaya (2009).
Multicomponent drug efflux complexes: architecture and mechanism of assembly.
  Future Microbiol, 4, 919-932.  
19026770 H.Nikaido, and Y.Takatsuka (2009).
Mechanisms of RND multidrug efflux pumps.
  Biochim Biophys Acta, 1794, 769-781.  
19231985 H.Nikaido (2009).
Multidrug resistance in bacteria.
  Annu Rev Biochem, 78, 119-146.  
18955484 H.T.Lin, V.N.Bavro, N.P.Barrera, H.M.Frankish, S.Velamakanni, H.W.van Veen, C.V.Robinson, M.I.Borges-Walmsley, and A.R.Walmsley (2009).
MacB ABC Transporter Is a Dimer Whose ATPase Activity and Macrolide-binding Capacity Are Regulated by the Membrane Fusion Protein MacA.
  J Biol Chem, 284, 1145-1154.  
19602147 J.Scherer, and D.H.Nies (2009).
CzcP is a novel efflux system contributing to transition metal resistance in Cupriavidus metallidurans CH34.
  Mol Microbiol, 73, 601-621.  
19416927 K.M.Pos (2009).
Trinity revealed: Stoichiometric complex assembly of a bacterial multidrug efflux pump.
  Proc Natl Acad Sci U S A, 106, 6893-6894.  
19307562 K.Nagano, and H.Nikaido (2009).
Kinetic behavior of the major multidrug efflux pump AcrB of Escherichia coli.
  Proc Natl Acad Sci U S A, 106, 5854-5858.  
19258536 L.Cuthbertson, I.L.Mainprize, J.H.Naismith, and C.Whitfield (2009).
Pivotal roles of the outer membrane polysaccharide export and polysaccharide copolymerase protein families in export of extracellular polysaccharides in gram-negative bacteria.
  Microbiol Mol Biol Rev, 73, 155-177.  
19342493 M.F.Symmons, E.Bokma, E.Koronakis, C.Hughes, and V.Koronakis (2009).
The assembled structure of a complete tripartite bacterial multidrug efflux pump.
  Proc Natl Acad Sci U S A, 106, 7173-7178.
PDB code: 2v4d
19578383 N.P.Barrera, S.C.Isaacson, M.Zhou, V.N.Bavro, A.Welch, T.A.Schaedler, M.A.Seeger, R.N.Miguel, V.M.Korkhov, H.W.van Veen, H.Venter, A.R.Walmsley, C.G.Tate, and C.V.Robinson (2009).
Mass spectrometry of membrane transporters reveals subunit stoichiometry and interactions.
  Nat Methods, 6, 585-587.  
19451626 N.Tal, and S.Schuldiner (2009).
A coordinated network of transporters with overlapping specificities provides a robust survival strategy.
  Proc Natl Acad Sci U S A, 106, 9051-9056.  
19433508 P.H.Lee, K.L.Kuo, P.Y.Chu, E.M.Liu, and J.H.Lin (2009).
SLITHER: a web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating through channels in membrane transporters.
  Nucleic Acids Res, 37, W559-W564.  
19426128 R.Krämer, and C.Ziegler (2009).
Regulative interactions of the osmosensing C-terminal domain in the trimeric glycine betaine transporter BetP from Corynebacterium glutamicum.
  Biol Chem, 390, 685-691.  
19289182 R.Misra, and V.N.Bavro (2009).
Assembly and transport mechanism of tripartite drug efflux systems.
  Biochim Biophys Acta, 1794, 817-825.  
19383457 R.Schulz, and U.Kleinekathöfer (2009).
Transitions between closed and open conformations of TolC: the effects of ions in simulations.
  Biophys J, 96, 3116-3125.  
19453279 T.Eicher, L.Brandstätter, and K.M.Pos (2009).
Structural and functional aspects of the multidrug efflux pump AcrB.
  Biol Chem, 390, 693-699.  
19678712 X.Z.Li, and H.Nikaido (2009).
Efflux-mediated drug resistance in bacteria: an update.
  Drugs, 69, 1555-1623.  
19060146 Y.Takatsuka, and H.Nikaido (2009).
Covalently linked trimer of the AcrB multidrug efflux pump provides support for the functional rotating mechanism.
  J Bacteriol, 191, 1729-1737.  
19788177 Z.Ma, F.E.Jacobsen, and D.P.Giedroc (2009).
Coordination chemistry of bacterial metal transport and sensing.
  Chem Rev, 109, 4644-4681.  
18535149 A.L.Davidson, E.Dassa, C.Orelle, and J.Chen (2008).
Structure, function, and evolution of bacterial ATP-binding cassette systems.
  Microbiol Mol Biol Rev, 72, 317.  
17729275 A.Rath, and C.M.Deber (2008).
Surface recognition elements of membrane protein oligomerization.
  Proteins, 70, 786-793.  
  18931428 D.Veesler, S.Blangy, C.Cambillau, and G.Sciara (2008).
There is a baby in the bath water: AcrB contamination is a major problem in membrane-protein crystallization.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 880-885.
PDB code: 3d9b
18024521 G.Krishnamoorthy, E.B.Tikhonova, and H.I.Zgurskaya (2008).
Fitting periplasmic membrane fusion proteins to inner membrane transporters: mutations that enable Escherichia coli AcrA to function with Pseudomonas aeruginosa MexB.
  J Bacteriol, 190, 691-698.  
18805970 H.Yamanaka, H.Kobayashi, E.Takahashi, and K.Okamoto (2008).
MacAB is involved in the secretion of Escherichia coli heat-stable enterotoxin II.
  J Bacteriol, 190, 7693-7698.  
18847219 I.Bagai, C.Rensing, N.J.Blackburn, and M.M.McEvoy (2008).
Direct metal transfer between periplasmic proteins identifies a bacterial copper chaperone.
  Biochemistry, 47, 11408-11414.  
18389081 I.Bunikis, K.Denker, Y.Ostberg, C.Andersen, R.Benz, and S.Bergström (2008).
An RND-type efflux system in Borrelia burgdorferi is involved in virulence and resistance to antimicrobial compounds.
  PLoS Pathog, 4, e1000009.  
18849422 J.A.Bohnert, S.Schuster, M.A.Seeger, E.Fähnrich, K.M.Pos, and W.V.Kern (2008).
Site-directed mutagenesis reveals putative substrate binding residues in the Escherichia coli RND efflux pump AcrB.
  J Bacteriol, 190, 8225-8229.  
18835894 L.Vaccaro, K.A.Scott, and M.S.Sansom (2008).
Gating at both ends and breathing in the middle: conformational dynamics of TolC.
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18223659 M.A.Seeger, C.von Ballmoos, T.Eicher, L.Brandstätter, F.Verrey, K.Diederichs, and K.M.Pos (2008).
Engineered disulfide bonds support the functional rotation mechanism of multidrug efflux pump AcrB.
  Nat Struct Mol Biol, 15, 199-205.  
18812515 M.S.Wilke, M.Heller, A.L.Creagh, C.A.Haynes, L.P.McIntosh, K.Poole, and N.C.Strynadka (2008).
The crystal structure of MexR from Pseudomonas aeruginosa in complex with its antirepressor ArmR.
  Proc Natl Acad Sci U S A, 105, 14832-14837.
PDB code: 3ech
18761695 S.K.Aoki, J.C.Malinverni, K.Jacoby, B.Thomas, R.Pamma, B.N.Trinh, S.Remers, J.Webb, B.A.Braaten, T.J.Silhavy, and D.A.Low (2008).
Contact-dependent growth inhibition requires the essential outer membrane protein BamA (YaeT) as the receptor and the inner membrane transport protein AcrB.
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18406332 V.N.Bavro, Z.Pietras, N.Furnham, L.Pérez-Cano, J.Fernández-Recio, X.Y.Pei, R.Misra, and B.Luisi (2008).
Assembly and channel opening in a bacterial drug efflux machine.
  Mol Cell, 30, 114-121.
PDB codes: 2vdd 2vde
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Substrate competition studies using whole-cell accumulation assays with the major tripartite multidrug efflux pumps of Escherichia coli.
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Multiple molecular mechanisms for multidrug resistance transporters.
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Crystal structure of the multidrug efflux transporter AcrB at 3.1A resolution reveals the N-terminal region with conserved amino acids.
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PDB code: 2i6w
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Assembly of the MexAB-OprM multidrug pump of Pseudomonas aeruginosa: component interactions defined by the study of pump mutant suppressors.
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PDB code: 2j8s
17566106 L.Bamber, M.Harding, M.Monné, D.J.Slotboom, and E.R.Kunji (2007).
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17452106 S.Schuldiner (2007).
When biochemistry meets structural biology: the cautionary tale of EmrE.
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Crystal structure of AcrB in complex with a single transmembrane subunit reveals another twist.
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PDB code: 2rdd
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Drug-induced conformational changes in multidrug efflux transporter AcrB from Haemophilus influenzae.
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17905989 Y.Takatsuka, and H.Nikaido (2007).
Site-directed disulfide cross-linking shows that cleft flexibility in the periplasmic domain is needed for the multidrug efflux pump AcrB of Escherichia coli.
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Structural biology: the ins and outs of drug transport.
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The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.