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PDBsum entry 1x2t
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Protein binding
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PDB id
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1x2t
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References listed in PDB file
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Key reference
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Title
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Ph-Dependent structural changes at ca(2+)-Binding sites of coagulation factor IX-Binding protein.
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Authors
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N.Suzuki,
Z.Fujimoto,
T.Morita,
A.Fukamizu,
H.Mizuno.
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Ref.
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J Mol Biol, 2005,
353,
80-87.
[DOI no: ]
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PubMed id
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Abstract
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Coagulation factor IX-binding protein, isolated from Trimeresurus flavoviridis
(IX-bp), is a C-type lectin-like protein. It is an anticoagulant consisting of
homologous subunits, A and B. Each subunit has a Ca(2+)-binding site with a
unique affinity (K(d) values of 14muM and 130muM at pH 7.5). These binding
characteristics are pH-dependent and, under acidic conditions, the Ca(2+)
binding of the low-affinity site was reduced considerably. In order to identify
which site has high affinity and to investigate the pH-dependent Ca(2+) release
mechanism, we have determined the crystal structures of IX-bp at pH 6.5 and pH
4.6 (apo form), and compared the Ca(2+)-binding sites with each other and with
those of the solved structures under alkaline conditions; pH 7.8 and pH 8.0
(complexed form). At pH 6.5, Glu43 in the Ca(2+)-binding site of subunit A
displayed two conformations. One (minor) is that in the alkaline state, and the
other (major) is that at pH 4.6. However, the corresponding Gln43 residue of
subunit B is in only a single conformation, which is almost identical with that
in the alkaline state. At pH 4.6, Glu43 of subunit A adopts a conformation
similar to that of the major conformer observed at pH 6.5, while Gln43 of
subunit B assumes a new conformation, and both Ca(2+) positions are occupied by
water molecules. These results showed that Glu43 of subunit A is much more
sensitive to protonation than Gln43 of subunit B, and the conformational change
of Glu43 occurs around pH6.5, which may correspond to the step of Ca(2+) release.
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Figure 2.
Figure 2. Stereoviews of ball-and stick models of the
Ca^2+-binding sites of (a) subunit A and (b) subunit B. The
models at pH 8.0, pH 6.5 and pH 4.6 are shown in cyan, orange
and magenta, respectively. Dotted lines in grey and green
indicate Ca^2+ coordination and hydrogen bonds, respectively.
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Figure 3.
Figure 3. Close-up views of pH-dependent conformational
changes of (a) GluA43 and (b) GlnB43 coordinating to the Ca^2+.
Conformational changes are shown by the rotation of torsion
angles. The models at pH 8.0, pH 6.5 and pH 4.6 are shown in
cyan, orange and magenta, respectively.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2005,
353,
80-87)
copyright 2005.
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