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PDBsum entry 2gj5
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Transport protein
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PDB id
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2gj5
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References listed in PDB file
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Key reference
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Title
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Crystal structure of a secondary vitamin d3 binding site of milk beta-Lactoglobulin.
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Authors
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M.C.Yang,
H.H.Guan,
M.Y.Liu,
Y.H.Lin,
J.M.Yang,
W.L.Chen,
C.J.Chen,
S.J.Mao.
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Ref.
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Proteins, 2008,
71,
1197-1210.
[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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Beta-lactoglobulin (beta-LG), one of the most investigated proteins, is a major
bovine milk protein with a predominantly beta structure. The structural function
of the only alpha-helix with three turns at the C-terminus is unknown. Vitamin
D(3) binds to the central calyx formed by the beta-strands. Whether there are
two vitamin D binding-sites in each beta-LG molecule has been a subject of
controversy. Here, we report a second vitamin D(3) binding site identified by
synchrotron X-ray diffraction (at 2.4 A resolution). In the central calyx
binding mode, the aliphatic tail of vitamin D(3) clearly inserts into the
binding cavity, where the 3-OH group of vitamin D(3) binds externally. The
electron density map suggests that the 3-OH group interacts with the carbonyl of
Lys-60 forming a hydrogen bond (2.97 A). The second binding site, however, is
near the surface at the C-terminus (residues 136-149) containing part of an
alpha-helix and a beta-strand I with 17.91 A in length, while the span of
vitamin D(3) is about 12.51 A. A remarkable feature of the second exosite is
that it combines an amphipathic alpha-helix providing nonpolar residues
(Phe-136, Ala-139, and Leu-140) and a beta-strand providing a nonpolar (Ile-147)
and a buried polar residue (Arg-148). They are linked by a hydrophobic loop
(Ala-142, Leu-143, Pro-144, and Met-145). Thus, the binding pocket furnishes
strong hydrophobic force to stabilize vitamin D(3) binding. This finding
provides a new insight into the interaction between vitamin D(3) and beta-LG, in
which the exosite may provide another route for the transport of vitamin D(3) in
vitamin D(3) fortified dairy products. Atomic coordinates for the crystal
structure of beta-LG-vitamin D(3) complex described in this work have been
deposited in the PDB (access code 2GJ5).
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Figure 8.
Figure 8. Superimposed structure of the exosite before and
after binding of vitamin D[3] and a diagram showing their
contacts of less than 3.8 Å. (A) Superimposing the current
model for vitamin D[3]-  -LG
(colored in gray) with previously described native -LG
(in red) (PDB code 1BSQ) in the exosite reveals that the overall
conformation is not substantially changed upon the binding of
vitamin D[3]. (B) The exosite is near the surface of C-terminal
 -helix
and -strand
I, where the 3-OH group of vitamin D[3] does not apparently form
hydrogen boding with -LG.
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Figure 9.
Figure 9. Amphipathic helix of -LG
and its interaction with vitamin D[3]. (A) The only -helix
region of -LG
is located between residues 130 and 141 (Fig. 1). Most
interestingly, the -helix
is oriented as amphipathic with all the charged residues
clustered on one side without an exception. (B) The crystal
structure reveals that the hydrophobic side of the -helix
forms a stable hydrophobic pocket with -strand
I. They are linked by a hydrophobic loop (residues 142-145) and
thus facilitate the binding to vitamin D[3]. The stereo view
shows that part of vitamin D[3] is near the surface,
particularly for the aliphatic tail, which is consistent with
that depicted in Figure 5.
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2008,
71,
1197-1210)
copyright 2008.
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