PDBsum entry 2vdd

Transport protein

PDB id: 2vdd

Contents

Protein chains

429 a.a. *

Metals

__K ×3

_CL ×3

Waters ×1

* Residue conservation analysis

PDB id:

2vdd

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. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k12. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.30Å R-factor: 0.239 R-free: 0.295

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

Date:

04-Oct-07 Release date: 22-Apr-08

Protein chains

P02930  (TOLC_ECOLI) -  Outer membrane protein TolC from Escherichia coli (strain K12)

Seq: 493 a.a.

Struc: 429 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

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.

ABSTRACT

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.