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PDBsum entry 2f33
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Metal binding protein
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PDB id
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2f33
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References listed in PDB file
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Key reference
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Title
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Structure, Binding interface and hydrophobic transitions of ca2+-Loaded calbindin-D(28k).
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Authors
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D.J.Kojetin,
R.A.Venters,
D.R.Kordys,
R.J.Thompson,
R.Kumar,
J.Cavanagh.
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Ref.
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Nat Struct Mol Biol, 2006,
13,
641-647.
[DOI no: ]
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PubMed id
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Abstract
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Calbindin-D(28K) is a Ca2+-binding protein, performing roles as both a calcium
buffer and calcium sensor. The NMR solution structure of Ca2+-loaded
calbindin-D(28K) reveals a single, globular fold consisting of six distinct
EF-hand subdomains, which coordinate Ca2+ in loops on EF1, EF3, EF4 and EF5.
Target peptides from Ran-binding protein M and myo-inositol monophosphatase,
along with a new target from procaspase-3, are shown to interact with the
protein on a surface comprised of alpha5 (EF3), alpha8 (EF4) and the EF2-EF3 and
EF4-EF5 loops. Fluorescence experiments reveal that calbindin-D(28K) adopts
discrete hydrophobic states as it binds Ca2+. The structure, binding interface
and hydrophobic characteristics of Ca2+-loaded calbindin-D(28K) provide the
first detailed insights into how this essential protein may function. This
structure is one of the largest high-resolution NMR structures and the largest
monomeric EF-hand protein to be solved to date.
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Figure 2.
Figure 2. Long-distance EF-hand pair-pair interactions. C
 superimposition
of the ten lowest-energy structures of Ca^2+-loaded
calbindin-D[28K], showing representative pair-pair interactions
between EF1-EF2 and EF3-EF4 (a,b), and EF3-EF4 and EF5-EF6
(c,d). There is a 180° rotation about the vertical axis
between a and b and between c and d.
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Figure 3.
Figure 3. Peptide titrations of Ca^2+-loaded calbindin-D[28K]
and binding interface. (a–c) Selected regions of the 2D
^1H[N]-^15N TROSY spectra of calbindin-D[28K] binding to target
peptides from (a) RanBPM (LASIKNR), (b) IMPase (ISSIKEKYPSHS)
and (c) the pro-domain of procaspase-3 (SKSIKNLEP). The spectra
were collected at peptide/protein ratios of 0:1 (black), 1:1
(green), 2:1 (dark blue), 4:1 (light blue), 8:1 (red) and 16:1
(pink). Residues showing chemical shift changes or line
broadening are affected by peptide binding. (d) RanBPM peptide
binding characteristics mapped onto the structure ensemble of
Ca^2+-loaded calbindin-D[28K], displayed as a PyMOL surface
plot. Residues are highlighted according to trends observed as
results of the peptide titration: red, peak linewidth broadening
and disappearance; yellow, substantial change in chemical shift;
blue, moderate linewidth broadening and change in chemical
shift; gray, residues unobservable at 25 °C owing to
conformational exchange on an intermediate NMR timescale.
Peptides derived from IMPase and procaspase-3 show similar
binding traits (see text).
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Mol Biol
(2006,
13,
641-647)
copyright 2006.
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