 |
PDBsum entry 2vdd
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Transport protein
|
PDB id
|
|
|
|
2vdd
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Assembly and channel opening in a bacterial drug efflux machine.
|
|
|
Authors
|
|
V.N.Bavro,
Z.Pietras,
N.Furnham,
L.Pérez-Cano,
J.Fernández-Recio,
X.Y.Pei,
R.Misra,
B.Luisi.
|
|
|
Ref.
|
|
Mol Cell, 2008,
30,
114-121.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
