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Contents |
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* Residue conservation analysis
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DOI no:
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Proc Natl Acad Sci U S A
99:5982-5987
(2002)
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PubMed id:
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Functional role of internal water molecules in rhodopsin revealed by X-ray crystallography.
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T.Okada,
Y.Fujiyoshi,
M.Silow,
J.Navarro,
E.M.Landau,
Y.Shichida.
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ABSTRACT
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Activation of G protein-coupled receptors (GPCRs) is triggered and regulated by
structural rearrangement of the transmembrane heptahelical bundle containing a
number of highly conserved residues. In rhodopsin, a prototypical GPCR, the
helical bundle accommodates an intrinsic inverse-agonist 11-cis-retinal, which
undergoes photo-isomerization to the all-trans form upon light absorption. Such
a trigger by the chromophore corresponds to binding of a diffusible ligand to
other GPCRs. Here we have explored the functional role of water molecules in the
transmembrane region of bovine rhodopsin by using x-ray diffraction to 2.6 A.
The structural model suggests that water molecules, which were observed in the
vicinity of highly conserved residues and in the retinal pocket, regulate the
activity of rhodopsin-like GPCRs and spectral tuning in visual pigments,
respectively. To confirm the physiological relevance of the structural findings,
we conducted single-crystal microspectrophotometry on rhodopsin packed in our
three-dimensional crystals and show that its spectroscopic properties are
similar to those previously found by using bovine rhodopsin in suspension or
membrane environment.
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Selected figure(s)
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Figure 1.
Fig. 1. (a) Global view of the transmembrane helical
region of the refined bovine rhodopsin structure. The
cytoplasmic surface is shown in the upper side. The four
water-binding sites (Wat1-4) include seven water molecules
(light blue spheres). Details of the sites are summarized in
Table 2. (b) Detailed view of the Wat1 site. The residues
surrounding Wat1a, -b, and -c are shown as ball-and-stick
representation in standard atom colors. Colors of the stick are
yellow for the conserved residues, cyan for Ala-124, and green
for Phe-261. Numbers in parentheses are according to ref. 18.
Figures were prepared with MOLSCRIPT (38) and RASTER3D (39).
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Figure 2.
Fig. 2. (a) View of the retinal-binding site and electron
densities for the two water molecules (Wat2a and Wat2b, red
spheres) found in the vicinity of retinal Schiff base.  A-weighted
F[o]  F[c] omit
map calculated for the waters at 2.6 Å is contoured at 4.0
with
positive densities in blue. The figure was prepared with SPDBV
(40). (b) Hydrogen bond network around the Schiff base. Retinal
and Lys-296 are shown in purple with the NZ position in blue,
and the surrounding residues are represented as ball-and-stick
figures in standard colors. Wat2a and Wat2b are shown as
light-blue spheres. Each of the distances (Å) is an
averaged value from molecule A and molecule B in an asymmetric
unit. The figure was prepared with MOLSCRIPT (38) and RASTER3D
(39).
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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