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PDBsum entry 3dwn
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Lipid transport
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PDB id
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3dwn
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References listed in PDB file
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Key reference
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Title
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Transmembrane passage of hydrophobic compounds through a protein channel wall.
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Authors
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E.M.Hearn,
D.R.Patel,
B.W.Lepore,
M.Indic,
B.Van den berg.
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Ref.
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Nature, 2009,
458,
367-370.
[DOI no: ]
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PubMed id
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Note: In the PDB file this reference is
annotated as "TO BE PUBLISHED". The citation details given above have
been manually determined.
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Abstract
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Membrane proteins that transport hydrophobic compounds have important roles in
multi-drug resistance and can cause a number of diseases, underscoring the
importance of protein-mediated transport of hydrophobic compounds. Hydrophobic
compounds readily partition into regular membrane lipid bilayers, and their
transport through an aqueous protein channel is energetically unfavourable.
Alternative transport models involving acquisition from the lipid bilayer by
lateral diffusion have been proposed for hydrophobic substrates. So far, all
transport proteins for which a lateral diffusion mechanism has been proposed
function as efflux pumps. Here we present the first example of a lateral
diffusion mechanism for the uptake of hydrophobic substrates by the Escherichia
coli outer membrane long-chain fatty acid transporter FadL. A FadL mutant in
which a lateral opening in the barrel wall is constricted, but which is
otherwise structurally identical to wild-type FadL, does not transport
substrates. A crystal structure of FadL from Pseudomonas aeruginosa shows that
the opening in the wall of the beta-barrel is conserved and delineates a long,
hydrophobic tunnel that could mediate substrate passage from the extracellular
environment, through the polar lipopolysaccharide layer and, by means of the
lateral opening in the barrel wall, into the lipid bilayer from where the
substrate can diffuse into the periplasm. Because FadL homologues are found in
pathogenic and biodegrading bacteria, our results have implications for
combating bacterial infections and bioremediating xenobiotics in the environment.
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Figure 3.
Figure 3: A hydrophobic passageway for substrate diffusion in
PaFadL. a, Superposition of EcFadL (green) and PaFadL (red),
showing the conservation of the lateral opening. b,
Superposition of the hatch domains. c, Stereo side view of
PaFadL, with the three bound C[8]E[4] detergent molecules
indicated in red. 2F[o]-F[c] density is shown as a blue mesh,
contoured at 2.0  .
The hatch domain is coloured green. The belts of aromatic
residues that delineate the polar–apolar interfaces of the
outer membrane are shown as orange stick models.
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Figure 4.
Figure 4: Proposed lateral diffusion model for the uptake of
hydrophobic substrates by FadL proteins. a, Substrate (red
hexagon) capture from the extracellular medium by a low-affinity
binding site (L)^15; b, diffusion of the substrate into an
adjacent high-affinity binding site H (blue)^15; c, spontaneous
conformational changes in the N terminus (purple) result in
substrate release and create a continuous passageway to the
barrel wall opening formed by the kink in strand S3. The
substrate diffuses laterally through the opening into the outer
membrane (OM). The polar part of the LPS, constituting the
principal barrier in the transport process, is shown in grey.
The extracellular milieu (E) is at the top and the periplasm (P)
is at the bottom.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
Nature
(2009,
458,
367-370)
copyright 2009.
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Secondary reference #1
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Title
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Crystal structure of the long-Chain fatty acid transporter fadl.
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Authors
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B.Van den berg,
P.N.Black,
W.M.Clemons,
T.A.Rapoport.
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Ref.
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Science, 2004,
304,
1506-1509.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. General overview of the FadL structure. (A) A ribbon
diagram of FadL viewed from the side. The putative position of
the membrane (M) boundary is indicated with horizontal lines,
with the extracellular side (E) at the top and the periplasm (P)
at the bottom. Strands are colored green, with strands 1 to 6
and 12 to 14 labeled. Loops and coil regions are shown in gray,
3[10] helices in blue, and  -helices in red.
The extracellular loops L3 and L4 are indicated. (B) Cutaway
view of FadL from the side, approximately 45° rotated
relative to (A). The N-terminal hatch domain (residues A1 to
R42) is indicated in purple, and the kink in strand S3 (residues
T99 to T106) in orange. (C) Overview of FadL viewed from the
side in gray, in a different orientation relative to (A) to show
the positions of the bound detergent molecules in one molecule
of the asymmetric unit. Two C[8]E[4] molecules (green) are
present in a groove (G) between L3 and L4, and an LDAO molecule
(yellow) is bound in a high-affinity binding pocket (P).
Nitrogen atoms are shown in blue, and oxygen atoms in red. All
figures were made in RIBBONS (32).
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Figure 3.
Fig. 3. Features of the hatch domain and of the barrel
implicated in conformational changes. (A) Close-up stereoview
from the side (with strands S9 and S10 removed for clarity),
showing the conformational changes in the N terminus that result
in substrate release from the high-affinity binding site (P).
The hatch domain (residues 1 to 42) in the monoclinic crystals
is shown in red, that in the hexagonal crystals in green. The
side chains of selected residues and the bound LDAO molecules
are shown (yellow, monoclinic crystal form; cyan, hexagonal
crystal form). (B) Stereoview from the extracellular side,
showing the differences in the N terminus between the monoclinic
(red) and hexagonal (green) crystals. The side chains of F3 and
Q4 are indicated, highlighting the movement and rotation of the
N terminus to create room underneath the LDAO molecule (yellow).
For clarity, only the LDAO molecule present in the monoclinic
crystal form is shown. (C) Stereoview of monoclinic FadL in the
same orientation as in (B). The side chains of His83, Gly143,
Gly212, and Asn33 and Pro34 of the highly conserved NPA sequence
are indicated in green, with oxygen atoms in red and nitrogen
atoms in blue. The LDAO molecule bound in the high-affinity
binding site is shown. The putative location of the channel is
indicated with an asterisk.
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The above figures are
reproduced from the cited reference
with permission from the AAAs
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