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PDBsum entry 2wc6
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Transport protein
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PDB id
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2wc6
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References listed in PDB file
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Key reference
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Title
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Characterisation of bombyx mori odorant-Binding proteins reveals that a 'General odorant-Binding protein' Discriminates between sex pheromone components.
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Authors
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J.J.Zhou,
G.Robertson,
X.He,
S.Dufour,
A.M.Hooper,
J.A.Pickett,
N.H.Keep,
L.M.Field.
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Ref.
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J Mol Biol, 2009,
389,
529-545.
[DOI no: ]
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PubMed id
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Abstract
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In many insect species odorant-binding proteins (OBPs) are thought to be
responsible for the transport of pheromones and other semiochemicals across the
sensillum lymph to the olfactory receptors (ORs) within the antennal sensilla.
In the silkworm Bombyx mori the OBPs are subdivided into three main subfamlies,
pheromone-binding proteins (PBPs), general odorant-binding proteins (GOBPs) and
antennal binding proteins (ABPs). We used the 'MotifSearch' algorithm to search
for genes encoding putative OBPs in B. mori and found 13, many fewer than are
found in the genomes of fruitflies and mosquitoes. The 13 genes include seven
new ABP-like OBPs as well as the previously identified PBPs (three), GOBPs (two)
and ABPx. Quantitative examination of transcript levels showed that BmorPBP1,
BmorGOBP1, BmorGOBP2 and BmorABPx are expressed at very high levels in the
antennae and so could be involved in olfaction. A new two-phase binding assay,
along with other established assays, showed that BmorPBP1, BmorPBP2, BmorGOBP2
and BmorABPx all bind to the B. mori sex pheromone component
(10E,12Z)-hexadecadien-1-ol (bombykol). BmorPBP1, BmorPBP2 and BmorABPx also
bind the pheromone component (10E,12Z)-hexadecadienal (bombykal) equally well,
whereas BmorGOBP2 can discriminate between bombykol and bombykal. X-ray
structures show that when bombykol is bound to BmorGOBP2 it adopts a different
conformation from that found when it binds to BmorPBP1. Binding to BmorGOBP2
involves hydrogen bonding to Arg110 rather than to the Ser56 as found for
BmorPBP1.
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Figure 8.
Fig. 8. 3D structures of BmorGOBPs with ligands. (a) A stereo
view of the BmorGOBP2 liganded and apo structures. Bombykol
(blue), bombykal (coral), (10E,12Z)-tetradecadien-1-ol (yellow),
(10E)-hexadecen-12-yn-1-ol (cyan), (8E,10Z)-hexadecadien-1-ol
(magenta), apo (black). The bombykol ligand is shown in sphere
representation. N and C termini and periodic residues are as
indicated in the right-hand image. (b) A stereo view of bombykol
plus water structure of BmorGOPB2 with the final 2F[obs] –
F[cal] map in pink contoured at 1.0σ clipped to the ligand and
water, and the F[obs] – F[cal] map before modelling the ligand
contoured at 2.3σ unclipped in green. The side chains of GOBP2
are shown in green. Ser56 and the bombykol of the SSM superposed
structure of BmorPBP1 (1dqe) are shown in blue. (c) The F[obs]
– F[cal] electron density maps (represented as blue
chickenwire) for the BmorGOBP2 ligands before the ligands were
added to the structure contoured at 2.3σ. (i) Bombykol
coordinated directly to Arg110 and to the main chain carbonyl of
Val66. (ii) Bombykol coordinated via a water molecule. (iii)
Bombykal, coordinated to a water molecule that is also
coordinated to Glu98. (iv) (8E,10Z)-Hexadecadien-1-ol,
coordinated both to Glu98 and water. (v)
(10E)-Hexadecen-12-yn-1-ol, coordinated to water and Glu98. (vi)
(10E,12Z)-Tetradecadien-1-ol, coordinated to Glu98 and water.
Hydrogen bonds are indicated as broken black lines as predicted
by the algorithm of the CCP4MG molecular graphics program.
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Figure 9.
Fig. 9. Superposition of BmorPBP1 (PDB code 1DQE) and
BmorGOBP2 to show structural differences. (a) A stereo pair of
BmorPBP1 (red), BmorGOBP2 (blue with regions of greatest
difference in light blue). The disulfide bonds are yellow. The
bombykol ligand is represented as cylinders and coloured light
blue for the BmorGOBP2-bound conformation and pink for the
BmorPBP1-bound conformation. The ligand hydrogen bonding
residues Ser56 for BmorPBP1 and Arg110 for BmorGOBP2 are shown
as green cylinders. (b) (i) Enlarged and simplified view of the
major structural difference in the rear entry region (C-termini
from residue 126 and residues 25-49). Features are coloured as
described above. A potentially important stabilising hydrogen
bonding network has been included for BmorPBP1 (Tyr41 and Glu32,
shown as pink cylinders). The equivalent Phe41 in BmorGOBP2
(shown as blue cylinders) is buried more deeply and occupies the
space of the helix in BmorPBP1. The equivalent region of
BmorGOBP2 bulges out to occupy the space filled by the
C-terminus of BmorPBP1. (ii) Cut-away view of the ligand-binding
pocket showing the key hydrogen bonds formed with the bombykol
hydroxyl. PBP1 in red/pink and GOBP2 in blue. Hydrogen bonding
side chains are in green. (c) A representation of the possible
hydrogen bonding modes of bombykol and bombykal with hydrogen
bonds shown as dotted lines. (i) The hydroxyl of bombykol able
to form hydrogen bonds to water and to Glu98; and (ii) the
aldehyde of bombykal able to form only a single hydrogen bond to
water.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2009,
389,
529-545)
copyright 2009.
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