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PDBsum entry 1k95
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Metal binding protein
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PDB id
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1k95
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Contents |
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* Residue conservation analysis
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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 of ca(2+)-Loaded human grancalcin.
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Authors
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J.Jia,
N.Borregaard,
K.Lollike,
M.Cygler.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2001,
57,
1843-1849.
[DOI no: ]
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PubMed id
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Abstract
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Grancalcin is a cytosolic Ca(2+)-binding protein originally identified in human
neutrophils. It belongs to a new class of EF-hand proteins, called PEF proteins,
which contain five EF-hand motifs. At the N-terminus of grancalcin there is a
approximately 50 residue-long segment rich in glycines and prolines. The fifth
EF-hand, unpaired within the monomer, provides a means for dimerization through
pairing with its counterpart in a second molecule. The structure of full-length
grancalcin in the apo form and with one EF3 within the dimer occupied by a
Ca(2+) ion have been determined. Although the N-terminal segment was present in
the molecule, this part was disordered in the crystals. Here, the structure of a
truncated form of grancalcin, which is lacking 52 N-terminal residues, in the
presence and absence of Ca(2+) is presented. In the Ca(2+)-bound form the ions
are found in the EF1 and EF3 hands. Binding of Ca(2+) to these two EF hands
produces only minor conformational changes, mostly within the EF1 Ca(2+)-binding
loop. This observation supports the hypothesis, formulated on the basis of the
structure of a homologous protein ALG-2 which shows significant differences in
the orientation of EF4 and EF5 compared with grancalcin, that calcium is a
necessary factor but not sufficient alone for inducing a significant
conformational change in PEF proteins.
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Figure 1.
Figure 1 (a) Stereoview of the C^  trace
of the des(1-52)grancalcin dimer. The side chains liganding
Ca^2+ ions are shown in full. The individual EF-hands are
differentiated by color. (b) Cartoon drawing of the dimer. The
second monomer is drawn in light blue. Figures prepared with
MOLSCRIPT (Kraulis, 1991[Kraulis, P. J. (1991). J. Appl. Cryst.
24, 946-950.]) and RASTER3D (Merritt & Bacon, 1997[Merritt, E.
A. & Bacon, D. J. (1997). Methods Enzymol. 277, 505-524.]). (c)
Alignment of the sequences of EF1-EF5.
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Figure 4.
Figure 4 Superposition of Ca^2+-bound des(1-52)grancalcin and
ALG-2. The superposition is based on EF4/5 only. Grancalcin is
shown in red, ALG-2 is blue and the ALG-2-bound peptide in cyan.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2001,
57,
1843-1849)
copyright 2001.
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Secondary reference #1
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Title
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Crystal structure of human grancalcin, A member of the penta-Ef-Hand protein family.
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Authors
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J.Jia,
Q.Han,
N.Borregaard,
K.Lollike,
M.Cygler.
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Ref.
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J Mol Biol, 2000,
300,
1271-1281.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3. EF-hands of grancalcin and their comparison with
calpain dVI. Grancalcin is shown in dark lines and calpain in
light gray, Ca^2+ is shown as gray sphere connected by dashed
lines to its ligands. (a) Superposition of EF1 of grancalcin and
Ca^2+-bound EF1 of calpain dVI. Only the C-terminal part of the
loop and helix F1 were used for superposition. The Ca^2+ of
calpain is shown as a sphere and the dashed lines mark its
ligands. The two small gray spheres are water molecules
liganding calcium. (b) Superposition of EF2 from grancalcin and
calpain domain VI. Note that in grancalcin the usual glutamate
in position -Z is replaced by Ala113. (c) Comparison of
Ca^2+-bound (dark) and Ca^2+-free EF3 from the Ca-grancalcin
(light). (d) Superposition of EF5 of grancalcin and calpain dVI.
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Figure 4.
Figure 4. (a) The stereo view of C^a tracing of grancalcin
dimer (blue) with a superimposed domain VI of rat calpain
(magenta). The view is along the symmetry axis of the dimer with
the EF1 near the viewer. The main difference between the two
proteins is in the positioning of EF1. (b) Electrostatic
potential for grancalcin dimer, same view as above. (c)
Electrostatic potential for calpain dVI in the same orientation
as grancalcin.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #2
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Title
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Crystallization and preliminary X-Ray analysis of human grancalcin, A novel cytosolic ca2+-Binding protein present in leukocytes.
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Authors
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Q.Han,
J.Jia,
Y.Li,
K.Lollike,
M.Cygler.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2000,
56,
772-774.
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PubMed id
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