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PDBsum entry 2i6w

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protein links
Transport protein PDB id
2i6w
Jmol PyMol
Contents
Protein chain
1019 a.a. *
* Residue conservation analysis
PDB id:
2i6w
Name: Transport protein
Title: Crystal structure of the multidrug efflux transporter acrb
Structure: Acriflavine resistance protein b. Chain: a. Other_details: membrane protein
Source: Escherichia coli. Organism_taxid: 469008. Strain: bl21(de3)
Resolution:
3.10Å     R-factor:   0.305     R-free:   0.341
Authors: D.Das,Q.S.Xu,S.H.Kim
Key ref: D.Das et al. (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. PubMed id: 17275331
Date:
29-Aug-06     Release date:   01-May-07    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P31224  (ACRB_ECOLI) -  Multidrug efflux pump subunit AcrB
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1049 a.a.
1019 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     5 terms  

 

 
J Struct Biol 158:494-502 (2007)
PubMed id: 17275331  
 
 
Crystal structure of the multidrug efflux transporter AcrB at 3.1A resolution reveals the N-terminal region with conserved amino acids.
D.Das, Q.S.Xu, J.Y.Lee, I.Ankoudinova, C.Huang, Y.Lou, A.DeGiovanni, R.Kim, S.H.Kim.
 
  ABSTRACT  
 
Crystal structures of the bacterial multidrug transporter AcrB in R32 and C2 space groups showing both symmetric and asymmetric trimeric assemblies, respectively, supplemented with biochemical investigations, have provided most of the structural basis for a molecular level understanding of the protein structure and mechanisms for substrate uptake and translocation carried out by this 114-kDa inner membrane protein. They suggest that AcrB captures ligands primarily from the periplasm. Substrates can also enter the inner cavity of the transporter from the cytoplasm, but the exact mechanism of this remains undefined. Analysis of the amino acid sequences of AcrB and its homologs revealed the presence of conserved residues at the N-terminus including two phenylalanines which may be exposed to the cytoplasm. Any potential role that these conserved residues may play in function has not been addressed by existing biochemical or structural studies. Since phenylalanine residues elsewhere in the protein have been implicated in ligand binding, we explored the structure of this N-terminal region to investigate structural determinants near the cytoplasmic opening that may mediate drug uptake. Our structure of AcrB in R32 space group reveals an N-terminus loop, reducing the diameter of the central opening to approximately 15 A as opposed to the previously reported value of approximately 30 A for crystal structures in this space group with disordered N-terminus. Recent structures of the AcrB in C2 space group have revealed a helical conformation of this N-terminus but have not discussed its possible implications. We present the crystal structure of AcrB that reveals the structure of the N-terminus containing the conserved residues. We hope that the structural information provides a structural basis for others to design further biochemical investigation of the role of this portion of AcrB in mediating cytoplasmic ligand discrimination and uptake.
 

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.  
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.  
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
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.  
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.  
19678712 X.Z.Li, and H.Nikaido (2009).
Efflux-mediated drug resistance in bacteria: an update.
  Drugs, 69, 1555-1623.  
  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
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.  
17720784 S.Moslavac, K.Nicolaisen, O.Mirus, F.Al Dehni, R.Pernil, E.Flores, I.Maldener, and E.Schleiff (2007).
A TolC-like protein is required for heterocyst development in Anabaena sp. strain PCC 7120.
  J Bacteriol, 189, 7887-7895.  
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
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.

 

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