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PDBsum entry 2f1m

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protein Protein-protein interface(s) links
Transport protein PDB id
2f1m
Jmol
Contents
Protein chains
229 a.a. *
247 a.a. *
Waters ×36
* Residue conservation analysis
PDB id:
2f1m
Name: Transport protein
Title: Conformational flexibility in the multidrug efflux system pr
Structure: Acriflavine resistance protein a. Chain: a, b, c, d. Fragment: residues 45-312. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Strain: jm109. Gene: acra, lir, mtca. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.71Å     R-factor:   0.239     R-free:   0.275
Authors: J.Mikolosko,K.Bobyk,H.I.Zgurskaya,P.Ghosh
Key ref:
J.Mikolosko et al. (2006). Conformational flexibility in the multidrug efflux system protein AcrA. Structure, 14, 577-587. PubMed id: 16531241 DOI: 10.1016/j.str.2005.11.015
Date:
14-Nov-05     Release date:   21-Mar-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AE06  (ACRA_ECOLI) -  Multidrug efflux pump subunit AcrA
Seq:
Struc:
397 a.a.
229 a.a.*
Protein chain
Pfam   ArchSchema ?
P0AE06  (ACRA_ECOLI) -  Multidrug efflux pump subunit AcrA
Seq:
Struc:
397 a.a.
247 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 7 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   1 term 
  Biological process     transmembrane transport   1 term 

 

 
DOI no: 10.1016/j.str.2005.11.015 Structure 14:577-587 (2006)
PubMed id: 16531241  
 
 
Conformational flexibility in the multidrug efflux system protein AcrA.
J.Mikolosko, K.Bobyk, H.I.Zgurskaya, P.Ghosh.
 
  ABSTRACT  
 
Intrinsic resistance to multiple drugs in many gram-negative bacterial pathogens is conferred by resistance nodulation cell division efflux pumps, which are composed of three essential components as typified by the extensively characterized Escherichia coli AcrA-AcrB-TolC system. The inner membrane drug:proton antiporter AcrB and the outer membrane channel TolC export chemically diverse compounds out of the bacterial cell, and require the activity of the third component, the periplasmic protein AcrA. The crystal structures of AcrB and TolC have previously been determined, and we complete the molecular picture of the efflux system by presenting the structure of a stable fragment of AcrA. The AcrA fragment resembles the elongated sickle shape of its homolog Pseudomonas aeruginosa MexA, being composed of three domains: beta-barrel, lipoyl, and alpha-helical hairpin. Notably, unsuspected conformational flexibility in the alpha-helical hairpin domain of AcrA is observed, which has potential mechanistic significance in coupling between AcrA conformations and TolC channel opening.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Comparison of the TolC and AcrA(45-312)-4M Coiled-Coils
The magnitude of conformational change predicted for the opening of the TolC channel coincides with the flexibility observed in the AcrA a-helical hairpin domain. The inner (yellow) and outer helices (blue) of TolC are shown superposed based on the internal structural repeat (residues 16-98 and 222-316). Below these are molecules B (red) and C (green) of AcrA(45-312)-4M, as superposed on the lipoyl domain. Direct engagement of AcrA and TolC is not modeled.
 
  The above figure is reprinted by permission from Cell Press: Structure (2006, 14, 577-587) copyright 2006.  
  Figure was selected by the author.  

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.
  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
21513873 C.Oswald, and K.M.Pos (2011).
Drug resistance: a periplasmic ménage à trois.
  Chem Biol, 18, 405-407.  
21513882 E.B.Tikhonova, Y.Yamada, and H.I.Zgurskaya (2011).
Sequential mechanism of assembly of multidrug efflux pump AcrAB-TolC.
  Chem Biol, 18, 454-463.  
21249122 R.Kulathila, R.Kulathila, M.Indic, and B.van den Berg (2011).
Crystal Structure of Escherichia coli CusC, the Outer Membrane Component of a Heavy Metal Efflux Pump.
  PLoS One, 6, e15610.
PDB code: 3pik
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
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.
  J Biol Chem, 286, 5484-5493.  
20583998 A.Welch, C.U.Awah, S.Jing, H.W.van Veen, and H.Venter (2010).
Promiscuous partnering and independent activity of MexB, the multidrug transporter protein from Pseudomonas aeruginosa.
  Biochem J, 430, 355-364.  
  20379386 A.Y.Xiao, J.Wang, and M.H.Saier (2010).
Bacterial Adaptor Membrane Fusion Proteins and the Structurally Dissimilar Outer Membrane Auxiliary Proteins Have Exchanged Central Domains in alpha-Proteobacteria.
  Int J Microbiol, 2010, 589391.  
20442961 E.H.Kim, C.Rensing, and M.M.McEvoy (2010).
Chaperone-mediated copper handling in the periplasm.
  Nat Prod Rep, 27, 711-719.  
20534468 F.De Angelis, J.K.Lee, J.D.O'Connell, L.J.Miercke, K.H.Verschueren, V.Srinivasan, C.Bauvois, C.Govaerts, R.A.Robbins, J.M.Ruysschaert, R.M.Stroud, and G.Vandenbussche (2010).
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
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
20581201 H.M.Kim, Y.Xu, M.Lee, S.Piao, S.H.Sim, N.C.Ha, and K.Lee (2010).
Functional relationships between the AcrA hairpin tip region and the TolC aperture tip region for the formation of the bacterial tripartite efflux pump AcrAB-TolC.
  J Bacteriol, 192, 4498-4503.  
20038594 H.S.Kim, D.Nagore, and H.Nikaido (2010).
Multidrug efflux pump MdtBC of Escherichia coli is active only as a B2C heterotrimer.
  J Bacteriol, 192, 1377-1386.  
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.
  Antimicrob Agents Chemother, 54, 3770-3775.  
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.
  Mol Microbiol, 75, 1468-1483.  
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.  
  21081915 X.Q.Yao, H.Kenzaki, S.Murakami, and S.Takada (2010).
Drug export and allosteric coupling in a multidrug transporter revealed by molecular simulations.
  Nat Commun, 1, 117.  
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
19805313 E.B.Tikhonova, V.Dastidar, V.V.Rybenkov, and H.I.Zgurskaya (2009).
Kinetic control of TolC recruitment by multidrug efflux complexes.
  Proc Natl Acad Sci U S A, 106, 16416-16421.  
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.  
19502391 J.L.Rosner, and R.G.Martin (2009).
An excretory function for the Escherichia coli outer membrane pore TolC: upregulation of marA and soxS transcription and Rob activity due to metabolites accumulated in tolC mutants.
  J Bacteriol, 191, 5283-5292.  
19744979 J.M.Blair, R.M.La Ragione, M.J.Woodward, and L.J.Piddock (2009).
Periplasmic adaptor protein AcrA has a distinct role in the antibiotic resistance and virulence of Salmonella enterica serovar Typhimurium.
  J Antimicrob Chemother, 64, 965-972.  
19129185 K.Larue, M.S.Kimber, R.Ford, and C.Whitfield (2009).
Biochemical and Structural Analysis of Bacterial O-antigen Chain Length Regulator Proteins Reveals a Conserved Quaternary Structure.
  J Biol Chem, 284, 7395-7403.  
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.  
19411330 Q.Ge, Y.Yamada, and H.Zgurskaya (2009).
The C-terminal domain of AcrA is essential for the assembly and function of the multidrug efflux pump AcrAB-TolC.
  J Bacteriol, 191, 4365-4371.  
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.  
19678712 X.Z.Li, and H.Nikaido (2009).
Efflux-mediated drug resistance in bacteria: an update.
  Drugs, 69, 1555-1623.  
19788177 Z.Ma, F.E.Jacobsen, and D.P.Giedroc (2009).
Coordination chemistry of bacterial metal transport and sensing.
  Chem Rev, 109, 4644-4681.  
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.  
18835894 L.Vaccaro, K.A.Scott, and M.S.Sansom (2008).
Gating at both ends and breathing in the middle: conformational dynamics of TolC.
  Biophys J, 95, 5681-5691.  
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.  
  18453709 S.Piao, Y.Xu, and N.C.Ha (2008).
Crystallization and preliminary X-ray crystallographic analysis of MacA from Actinobacillus actinomycetemcomitans.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 391-393.  
18485072 T.Gristwood, P.C.Fineran, L.Everson, and G.P.Salmond (2008).
PigZ, a TetR/AcrR family repressor, modulates secondary metabolism via the expression of a putative four-component resistance-nodulation-cell-division efflux pump, ZrpADBC, in Serratia sp. ATCC 39006.
  Mol Microbiol, 69, 418-435.  
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
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
17214741 E.B.Tikhonova, V.K.Devroy, S.Y.Lau, and H.I.Zgurskaya (2007).
Reconstitution of the Escherichia coli macrolide transporter: the periplasmic membrane fusion protein MacA stimulates the ATPase activity of MacB.
  Mol Microbiol, 63, 895-910.  
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
17893146 I.Bagai, W.Liu, C.Rensing, N.J.Blackburn, and M.M.McEvoy (2007).
Substrate-linked conformational change in the periplasmic component of a Cu(I)/Ag(I) efflux system.
  J Biol Chem, 282, 35695-35702.  
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
17665187 S.Trépout, J.C.Taveau, S.Mornet, H.Benabdelhak, A.Ducruix, and O.Lambert (2007).
Organization of reconstituted lipoprotein MexA onto supported lipid membrane.
  Eur Biophys J, 36, 1029-1037.  
17720796 T.Mima, S.Joshi, M.Gomez-Escalada, and H.P.Schweizer (2007).
Identification and characterization of TriABC-OpmH, a triclosan efflux pump of Pseudomonas aeruginosa requiring two membrane fusion proteins.
  J Bacteriol, 189, 7600-7609.  
16648168 L.Vaccaro, V.Koronakis, and M.S.Sansom (2006).
Flexibility in a drug transport accessory protein: molecular dynamics simulations of MexA.
  Biophys J, 91, 558-564.  
16946072 M.A.Seeger, A.Schiefner, T.Eicher, F.Verrey, K.Diederichs, and K.M.Pos (2006).
Structural asymmetry of AcrB trimer suggests a peristaltic pump mechanism.
  Science, 313, 1295-1298.
PDB codes: 2gif 2hrt
16915237 S.Murakami, R.Nakashima, E.Yamashita, T.Matsumoto, and A.Yamaguchi (2006).
Crystal structures of a multidrug transporter reveal a functionally rotating mechanism.
  Nature, 443, 173-179.
PDB codes: 2dhh 2dr6 2drd
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.