PDBsum entry 2vde

Go to PDB code: 
protein metals Protein-protein interface(s) links
Transport protein PDB id
Protein chains
429 a.a. *
_CL ×4
* Residue conservation analysis
PDB id:
Name: Transport protein
Title: Crystal structure of the open state of tolc outer membrane component of mutlidrug efflux pumps
Structure: Outer membrane protein tolc. Chain: a, b, c. Fragment: residues 1-450. Synonym: tolc. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Expressed in: escherichia coli. Expression_system_taxid: 562.
3.20Å     R-factor:   0.268     R-free:   0.315
Authors: V.N.Bavro,Z.Pietras,N.Furnham,L.Perez-Cano, J.Fernandez-Recio,X.Y.Pei,R.Truer,R.Misra,B.Luisi
Key ref:
V.N.Bavro et al. (2008). Assembly and channel opening in a bacterial drug efflux machine. Mol Cell, 30, 114-121. PubMed id: 18406332 DOI: 10.1016/j.molcel.2008.02.015
04-Oct-07     Release date:   22-Apr-08    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P02930  (TOLC_ECOLI) -  Outer membrane protein TolC
493 a.a.
429 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     outer membrane   1 term 
  Biological process     transport   2 terms 
  Biochemical function     transporter activity     1 term  


DOI no: 10.1016/j.molcel.2008.02.015 Mol Cell 30:114-121 (2008)
PubMed id: 18406332  
Assembly and channel opening in a bacterial drug efflux machine.
V.N.Bavro, Z.Pietras, N.Furnham, L.Pérez-Cano, J.Fernández-Recio, X.Y.Pei, R.Misra, B.Luisi.
Drugs and certain proteins are transported across the membranes of Gram-negative bacteria by energy-activated pumps. The outer membrane component of these pumps is a channel that opens from a sealed resting state during the transport process. We describe two crystal structures of the Escherichia coli outer membrane protein TolC in its partially open state. Opening is accompanied by the exposure of three shallow intraprotomer grooves in the TolC trimer, where our mutagenesis data identify a contact point with the periplasmic component of a drug efflux pump, AcrA. We suggest that the assembly of multidrug efflux pumps is accompanied by induced fit of TolC driven mainly by accommodation of the periplasmic component.
  Selected figure(s)  
Figure 1.
The TolC Outer Membrane Protein and Its Partial Opening (A) A side view of the TolC homotrimer (1EK9). (B) A schematic of the mutations that were studied here to stabilize channel opening. A network of charged interactions maintaining the resting closed state of TolC (1EK9). These include Y362, R367 from H7/H8, which are coordinated by T152, and D153 from H3/H4. Y362 has been mutated to F and R367 to E to disrupt the network of salt bridges (shown in bold). The protomers are colored red, blue, and green. (C) Crystal structures of the open and closed states. The view is along the trifold axis at the periplasmic, AcrB-engaging end of the TolC trimer. (D) Helical movements from the open to the closed state for the two crystal forms. Transition of the mobile helices H7/H8 from closed state (orange) to open as exemplified by the different subunits of C2 (cyan and green) and P2[1]2[1]2[1] (gray and yellow). The view is of overlays of helical fragments H7/H8 (foreground) and H3/H4 (background), revealing the minimal relative movement of H3/H4 static helices as compared with H7/H8. (E) Top view of the same overlays shown in (D). The displacement of the H7 helix is up to 11 A in the C2 structure. Note also the lagging of the H8 helices and the relative swing of the H7 in respect to H8. The triangle indicates the molecular trifold axis. Mol Cell. 2008 April 11; 30(1): 114–121. doi: 10.1016/j.molcel.2008.02.015. Copyright [copyright] 2008 ELL & Excerpta Medica
Figure 2.
Potential Docking Faces of the Partially Opened State of TolC (A and B) The second aperture of the channel is less perturbed in the crystal structures of the partially opened state. A cross-section through the TolC channel in the closed-state (A) and open-state C2 crystal form (B) at the level of the second selectivity filter formed by the ring of D374 residues. While the outer opening of the channel (as measured by the position of G365) from the 8.5 A in closed state to about 20 A in the C2 form (Figure 1 Figure 1-C, Figure S2), the interior second selectivity filter composed of a ring of D374 deeper in the channel is much less perturbed. Although the distance between the D374 is extended from about 6.1 A in 1EK9 to up to 8.4 A in the C2 form, it is unlikely to be sufficient for even small molecules to pass unimpeded, thus suggesting that a further opening of the channel is required for transport. This is likely to be activated by the engagement of the periplasmic partner protein, AcrA. Note the deepening of the predicted AcrA binding groove in the partially open C2 structure. (C) The intermesh of the loops in the packing of the TolC open state, showing details of the trimer-trimer contact interface across a crystallographic symmetry operation in the C2 crystal form. This interaction may mimic the docking of the TolC into the matching surface of the AcrB (shown in [D]). (D) Docking model of AcrB and a model of open-state TolC based on the C2 crystal structure. Colored by chain. The model of the AcrB-TolC complex was prepared using the asymmetric structures (2GIF and C2 crystal form of TolC). Although [beta]2 hairpin is in proximity of H7/H8, it is still capable of interacting with the H3/H4 residues, in agreement with crosslinking data (Tamura et al., 2005). Residues indicated by arrows are D153, one of the residues included in TolC wild-type that maintains the closed gate; D795 from AcrB, a residue from AcrB [beta]2 hairpin, which could potentially disrupt D153 interactions; and Y362 (another gating residue from TolC) and D256 (from [beta]1 hairpin of AcrB), which in our refined docking model are close to the interface. Mol Cell. 2008 April 11; 30(1): 114–121. doi: 10.1016/j.molcel.2008.02.015. Copyright [copyright] 2008 ELL & Excerpta Medica
  The above figures are reprinted from an Open Access publication published by Cell Press: Mol Cell (2008, 30, 114-121) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
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.  
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.
  Proc Natl Acad Sci U S A, 108, 2112-2117.
PDB codes: 2wmz 2xmn
21371926 Y.S.Choong, T.S.Lim, A.L.Chew, I.Aziah, and A.Ismail (2011).
Structural and functional studies of a 50 kDa antigenic protein from Salmonella enterica serovar Typhi.
  J Mol Graph Model, 29, 834-842.  
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.  
21221942 B.Y.Yun, Y.Xu, S.Piao, N.Kim, J.H.Yoon, H.S.Cho, K.Lee, and N.C.Ha (2010).
Periplasmic domain of CusA in an Escherichia coli Cu+/Ag+ transporter has metal binding sites.
  J Microbiol, 48, 829-835.  
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.  
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.  
20805930 M.J.Dunlop, J.D.Keasling, and A.Mukhopadhyay (2010).
A model for improving microbial biofuel production using a synthetic feedback loop.
  Syst Synth Biol, 4, 95.  
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.  
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.  
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
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.  
19500339 R.Villa, M.Lotti, and P.Gatti-Lafranconi (2009).
Components of the E. coli envelope are affected by and can react to protein over-production in the cytoplasm.
  Microb Cell Fact, 8, 32.  
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.  
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.  
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.  
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.