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PDBsum entry 1t9v

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protein ligands links
Membrane protein PDB id
1t9v
Jmol
Contents
Protein chain
1014 a.a. *
Ligands
RHQ ×2
* Residue conservation analysis
PDB id:
1t9v
Name: Membrane protein
Title: Structural basis of multidrug transport by the acrb multidru pump
Structure: Acriflavine resistance protein b. Chain: a. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: acrb, acre, b0462. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Trimer (from PQS)
Resolution:
3.80Å     R-factor:   0.278     R-free:   0.331
Authors: E.W.Yu,G.Mcdermott,H.Nikaido
Key ref: E.W.Yu et al. (2005). A periplasmic drug-binding site of the AcrB multidrug efflux pump: a crystallographic and site-directed mutagenesis study. J Bacteriol, 187, 6804-6815. PubMed id: 16166543
Date:
18-May-04     Release date:   04-Oct-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P31224  (ACRB_ECOLI) -  Multidrug efflux pump subunit AcrB
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1049 a.a.
1014 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

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

 

 
J Bacteriol 187:6804-6815 (2005)
PubMed id: 16166543  
 
 
A periplasmic drug-binding site of the AcrB multidrug efflux pump: a crystallographic and site-directed mutagenesis study.
E.W.Yu, J.R.Aires, G.McDermott, H.Nikaido.
 
  ABSTRACT  
 
The Escherichia coli AcrB multidrug efflux pump is a membrane protein that recognizes many structurally dissimilar toxic compounds. We previously reported the X-ray structures of four AcrB-ligand complexes in which the ligands were bound to the wall of the extremely large central cavity in the transmembrane domain of the pump. Genetic studies, however, suggested that discrimination between the substrates occurs mainly in the periplasmic domain rather than the transmembrane domain of the pump. We here describe the crystal structures of the AcrB mutant in which Asn109 was replaced by Ala, with five structurally diverse ligands, ethidium, rhodamine 6G, ciprofloxacin, nafcillin, and Phe-Arg-beta-naphthylamide. The ligands bind not only to the wall of central cavity but also to a new periplasmic site within the deep external depression formed by the C-terminal periplasmic loop. This depression also includes residues identified earlier as being important in the specificity. We show here that conversion into alanine of the Phe664, Phe666, or Glu673 residue in the periplasmic binding site produced significant decreases in the MIC of most agents in the N109A background. Furthermore, decreased MICs were also observed when these residues were mutated in the wild-type AcrB background, although the effects were more modest. The MIC data were also confirmed by assays of ethidium influx rates in intact cells, and our results suggest that the periplasmic binding site plays a role in the physiological process of drug efflux.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21071494 A.Mahamoud, J.Chevalier, M.Baitiche, E.Adam, and J.M.Pagès (2011).
An alkylaminoquinazoline restores antibiotic activity in Gram-negative resistant isolates.
  Microbiology, 157, 566-571.  
20981744 C.C.Su, F.Long, and E.W.Yu (2011).
The Cus efflux system removes toxic ions via a methionine shuttle.
  Protein Sci, 20, 6.  
21350490 C.C.Su, F.Long, M.T.Zimmermann, K.R.Rajashankar, R.L.Jernigan, and E.W.Yu (2011).
Crystal structure of the CusBA heavy-metal efflux complex of Escherichia coli.
  Nature, 470, 558-562.
PDB code: 3ne5
21549704 J.M.Bolla, S.Alibert-Franco, J.Handzlik, J.Chevalier, A.Mahamoud, G.Boyer, K.Kieć-Kononowicz, and J.M.Pagès (2011).
Strategies for bypassing the membrane barrier in multidrug resistant Gram-negative bacteria.
  FEBS Lett, 585, 1682-1690.  
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.
  Nature, 480, 565-569.
PDB codes: 3aoa 3aob 3aoc 3aod
20038628 C.A.Elkins, L.B.Mullis, D.W.Lacher, and C.M.Jung (2010).
Single nucleotide polymorphism analysis of the major tripartite multidrug efflux pump of Escherichia coli: functional conservation in disparate animal reservoirs despite exposure to antimicrobial chemotherapy.
  Antimicrob Agents Chemother, 54, 1007-1015.  
20525265 E.Perrin, M.Fondi, M.C.Papaleo, I.Maida, S.Buroni, M.R.Pasca, G.Riccardi, and R.Fani (2010).
Exploring the HME and HAE1 efflux systems in the genus Burkholderia.
  BMC Evol Biol, 10, 164.  
20804453 F.Husain, and H.Nikaido (2010).
Substrate path in the AcrB multidrug efflux pump of Escherichia coli.
  Mol Microbiol, 78, 320-330.  
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.
  Structure, 18, 507-517.
PDB code: 3d5k
20513705 N.G.Coldham, M.Webber, M.J.Woodward, and L.J.Piddock (2010).
A 96-well plate fluorescence assay for assessment of cellular permeability and active efflux in Salmonella enterica serovar Typhimurium and Escherichia coli.
  J Antimicrob Chemother, 65, 1655-1663.  
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.
  Proc Natl Acad Sci U S A, 107, 6559-6565.  
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.  
19201794 F.A.Martin, D.M.Posadas, M.C.Carrica, S.L.Cravero, D.O'Callaghan, and A.Zorreguieta (2009).
Interplay between two RND systems mediating antimicrobial resistance in Brucella suis.
  J Bacteriol, 191, 2530-2540.  
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.  
19279676 J.M.Pages, J.P.Lavigne, V.Leflon-Guibout, E.Marcon, F.Bert, L.Noussair, and M.H.Nicolas-Chanoine (2009).
Efflux pump, the masked side of beta-lactam resistance in Klebsiella pneumoniae clinical isolates.
  PLoS ONE, 4, e4817.  
19649280 L.Mamelli, S.Petit, J.Chevalier, C.Giglione, A.Lieutaud, T.Meinnel, I.Artaud, and J.M.Pagès (2009).
New antibiotic molecules: bypassing the membrane barrier of gram negative bacteria increases the activity of peptide deformylase inhibitors.
  PLoS One, 4, e6443.  
19164140 Q.T.Tran, M.Dupont, J.P.Lavigne, J.Chevalier, J.M.Pagès, A.Sotto, and A.Davin-Regli (2009).
Occurrence of efflux mechanism and cephalosporinase variant in a population of Enterobacter aerogenes and Klebsiella pneumoniae isolates producing extended-spectrum beta-lactamases.
  Antimicrob Agents Chemother, 53, 1652-1656.  
19289182 R.Misra, and V.N.Bavro (2009).
Assembly and transport mechanism of tripartite drug efflux systems.
  Biochim Biophys Acta, 1794, 817-825.  
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.  
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.  
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.  
17210767 C.A.Elkins, and L.B.Mullis (2007).
Substrate competition studies using whole-cell accumulation assays with the major tripartite multidrug efflux pumps of Escherichia coli.
  Antimicrob Agents Chemother, 51, 923-929.  
17910961 C.C.Su, H.Nikaido, and E.W.Yu (2007).
Ligand-transporter interaction in the AcrB multidrug efflux pump determined by fluorescence polarization assay.
  FEBS Lett, 581, 4972-4976.  
17275331 D.Das, Q.S.Xu, J.Y.Lee, I.Ankoudinova, C.Huang, Y.Lou, A.DeGiovanni, R.Kim, and S.H.Kim (2007).
Crystal structure of the multidrug efflux transporter AcrB at 3.1A resolution reveals the N-terminal region with conserved amino acids.
  J Struct Biol, 158, 494-502.
PDB code: 2i6w
17194213 G.Sennhauser, P.Amstutz, C.Briand, O.Storchenegger, and M.G.Grütter (2007).
Drug export pathway of multidrug exporter AcrB revealed by DARPin inhibitors.
  PLoS Biol, 5, e7.
PDB code: 2j8s
17159924 O.Lomovskaya, H.I.Zgurskaya, M.Totrov, and W.J.Watkins (2007).
Waltzing transporters and 'the dance macabre' between humans and bacteria.
  Nat Rev Drug Discov, 6, 56-65.  
18073115 S.Törnroth-Horsefield, P.Gourdon, R.Horsefield, L.Brive, N.Yamamoto, H.Mori, A.Snijder, and R.Neutze (2007).
Crystal structure of AcrB in complex with a single transmembrane subunit reveals another twist.
  Structure, 15, 1663-1673.
PDB code: 2rdd
17526713 V.Dastidar, W.Mao, O.Lomovskaya, and H.I.Zgurskaya (2007).
Drug-induced conformational changes in multidrug efflux transporter AcrB from Haemophilus influenzae.
  J Bacteriol, 189, 5550-5558.  
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.
  J Bacteriol, 189, 8677-8684.  
17015668 C.C.Su, M.Li, R.Gu, Y.Takatsuka, G.McDermott, H.Nikaido, and E.W.Yu (2006).
Conformation of the AcrB multidrug efflux pump in mutants of the putative proton relay pathway.
  J Bacteriol, 188, 7290-7296.
PDB codes: 2hqc 2hqd 2hqf 2hqg
16352827 E.M.Hearn, M.R.Gray, and J.M.Foght (2006).
Mutations in the central cavity and periplasmic domain affect efflux activity of the resistance-nodulation-division pump EmhB from Pseudomonas fluorescens cLP6a.
  J Bacteriol, 188, 115-123.  
16614254 L.J.Piddock (2006).
Clinically relevant chromosomally encoded multidrug resistance efflux pumps in bacteria.
  Clin Microbiol Rev, 19, 382-402.  
16288462 W.C.Lu, C.Z.Wang, E.W.Yu, and K.M.Ho (2006).
Dynamics of the trimeric AcrB transporter protein inferred from a B-factor analysis of the crystal structure.
  Proteins, 62, 152-158.  
17015667 Y.Takatsuka, and H.Nikaido (2006).
Threonine-978 in the transmembrane segment of the multidrug efflux pump AcrB of Escherichia coli is crucial for drug transport as a probable component of the proton relay network.
  J Bacteriol, 188, 7284-7289.  
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.