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PDBsum entry 1dsy
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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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Ca(2+) bridges the c2 membrane-Binding domain of protein kinase calpha directly to phosphatidylserine.
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Authors
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N.Verdaguer,
S.Corbalan-Garcia,
W.F.Ochoa,
I.Fita,
J.C.Gómez-Fernández.
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Ref.
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EMBO J, 1999,
18,
6329-6338.
[DOI no: ]
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PubMed id
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Abstract
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The C2 domain acts as a membrane-targeting module in a diverse group of proteins
including classical protein kinase Cs (PKCs), where it plays an essential role
in activation via calcium-dependent interactions with phosphatidylserine. The
three-dimensional structures of the Ca(2+)-bound forms of the PKCalpha-C2 domain
both in the absence and presence of 1, 2-dicaproyl-sn-phosphatidyl-L-serine have
now been determined by X-ray crystallography at 2.4 and 2.6 A resolution,
respectively. In the structure of the C2 ternary complex, the
glycerophosphoserine moiety of the phospholipid adopts a quasi-cyclic
conformation, with the phosphoryl group directly coordinated to one of the
Ca(2+) ions. Specific recognition of the phosphatidylserine is reinforced by
additional hydrogen bonds and hydrophobic interactions with protein residues in
the vicinity of the Ca(2+) binding region. The central feature of the
PKCalpha-C2 domain structure is an eight-stranded, anti-parallel beta-barrel
with a molecular topology and organization of the Ca(2+) binding region closely
related to that found in PKCbeta-C2, although only two Ca(2+) ions have been
located bound to the PKCalpha-C2 domain. The structural information provided by
these results suggests a membrane binding mechanism of the PKCalpha-C2 domain in
which calcium ions directly mediate the phosphatidylserine recognition while the
calcium binding region 3 might penetrate into the phospholipid bilayer.
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Figure 1.
Figure 1 (A) Overall structure of the C2 domain of PKC  bound
to PS.  -strands
are depicted as arrows numbered sequentially. The two Ca^2+ ions
located in the calcium binding site are also shown as orange
spheres. The DCPS and phosphate molecules found in the ternary
complex are explicitly shown as balls and sticks. (B) Surface
potential drawing of the PKC -C2
-Ca^2+ domain structure as computed and displayed by GRASP
(Nicholls et al., 1991). Positively and negatively charged
regions are shown in blue and red, respectively. The DCPS- and
phosphate-bound molecules are also depicted as stick models.
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Figure 3.
Figure 3 (A) Stereoviews of the F[o]-F[c] omit map of the
ternary complex at 2.6 Å resolution, in the vicinity of Ca1
contoured at 2  .
All the atoms corresponding to residues Asn189, Arg216, Arg249,
Thr251 and also to the ion Ca1 and to the DCPS ligand were
omitted for the map calculation according to the CNS protocols.
The molecular fragments modeled into the corresponding density
are also shown. The DCPS ligand is represented with the
conformation corresponding to the sn-2 model (see the text). (B)
Stereoviews, in the same orientation as in (A), of the F[o]-F[c]
omit map (blue) of the ternary complex calculated omitting only
the DCPS ligand. The residual F[o]-F[c] map calculated from the
final refined model is also shown superimposed together with the
DCPS model. Only some positive density (red) could be seen close
to the position corresponding to the phosphoryl moiety. All the
map contouring shown was carried out 2.5 .
(C) The superimposition of the two alternative DCPS
conformations (sn-1 in purple and sn-2 in green) emphasizes the
similar atomic disposition.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(1999,
18,
6329-6338)
copyright 1999.
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