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PDBsum entry 1ocs
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Sorting protein
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PDB id
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1ocs
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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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Crystal structure of the yeast phox homology (px) domain protein grd19p complexed to phosphatidylinositol-3-Phosphate.
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Authors
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C.Z.Zhou,
I.L.De la sierra-Gallay,
S.Quevillon-Cheruel,
B.Collinet,
P.Minard,
K.Blondeau,
G.Henckes,
R.Aufrère,
N.Leulliot,
M.Graille,
I.Sorel,
P.Savarin,
F.De la torre,
A.Poupon,
J.Janin,
H.Van tilbeurgh.
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Ref.
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J Biol Chem, 2003,
278,
50371-50376.
[DOI no: ]
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PubMed id
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Abstract
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Phox homology (PX) domains have been recently identified in a number of
different proteins and are involved in various cellular functions such as
vacuolar targeting and membrane protein trafficking. It was shown that these
modules of about 130 amino acids specifically binding to phosphoinositides and
that this interaction is crucial for their cellular function. The yeast genome
contains 17 PX domain proteins. One of these, Grd19p, is involved in the
localization of the late Golgi membrane proteins DPAP A and Kex2p. Grd19p
consists of the PX domain with 30 extra residues at the N-terminal and is
homologous to the functionally characterized human sorting nexin protein SNX3.
We determined the 2.0 A crystal structure of Grd19p in the free form and in
complex with d-myo-phosphatidylinositol 3-phosphate (diC4PtdIns(3)P),
representing the first case of both free and ligand-bound conformations of the
same PX module. The ligand occupies a well defined positively charged binding
pocket at the interface between the beta-sheet and alpha-helical parts of the
molecule. The structure of the free and bound protein are globally similar but
show some significant differences in a region containing a polyproline peptide
and a putative membrane attachment site.
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Figure 3.
FIG. 3. A, stereo view of an omitted F[o] - F[c] electron
density map covering the bound diC4PtdIns(3)P, contoured at 3
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B, overall view of binding of diC4PtdIns(3)P to Grd19p. Helices
are colored yellow, strands green, and loop connections purple.
The ligand is represented in sticks (gray, carbon; red, oxygen;
and pink, phosphate). Some of the secondary structure elements
(Fig. 1) are labeled. C, detailed stereo view of diC4PtdIns(3)P
binding to Grd19p (yellow, carbon atoms; green, phosphate; red,
oxygen; and blue, nitrogen). Positions of the phosphate groups
of the ligand on the 1- and 3-OH position are labeled as P1 and
P3, respectively.
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Figure 4.
FIG. 4. A, stereo view of the superposition of the
ligand-bound (C atoms in yellow) and free form (C atoms in
wheat) of Grd19p. Residues in a radius of 5 Å around the
bound ligand are represented. B, stereo view of the
superposition of the ligand-binding sites of Grd19p and
p40^phox. Grd19p, same color code as Fig. 4A. p40^phox has
carbon atoms in green. Only the Grd19p residues are labeled.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2003,
278,
50371-50376)
copyright 2003.
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