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PDBsum entry 1gnu
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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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The X-Ray crystal structure and putative ligand-Derived peptide binding properties of gamma-Aminobutyric acid receptor type a receptor-Associated protein.
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Authors
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D.Knight,
R.Harris,
M.S.Mcalister,
J.P.Phelan,
S.Geddes,
S.J.Moss,
P.C.Driscoll,
N.H.Keep.
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Ref.
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J Biol Chem, 2002,
277,
5556-5561.
[DOI no: ]
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PubMed id
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Abstract
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The gamma-aminobutyric acid receptor type A (GABA(A)) receptor-associated
protein (GABARAP) has been reported to mediate the interaction between the
GABA(A) receptor and microtubules. We present the three-dimensional structure of
GABARAP obtained by x-ray diffraction at 1.75 A resolution. The structure was
determined by molecular replacement using the structure of the homologous
protein GATE-16. NMR spectroscopy of isotope-labeled GABARAP showed the
structure in solution to be compatible with the overall fold but showed evidence
of conformation heterogeneity that is not apparent in the crystal structure. We
assessed the binding of GABARAP to peptides derived from reported binding
partner proteins, including the M3-M4 loop of the gamma2 subunit of the GABA(A)
receptor and the acidic carboxyl-terminal tails of human alpha- and
beta-tubulin. There is a small area of concentrated positive charge on one
surface of GABARAP, which we found interacts weakly with all peptides tested,
but we found no evidence for specific binding to the proposed physiological
target peptides. These results are compatible with a more general role in
membrane targeting and transportation for the GABARAP family of proteins.
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Figure 1.
Fig. 1. a, stereo representation of the superposition of
the GABARAP and GATE-16 main chains. b, cartoon diagram of the
GABARAP three-dimensional backbone structure. Region 1-35 is in
green, region 35-68 is in red, and region 68-117 is in blue.
Therefore, the baits used in the two hybrids are the 35-117
region (colored in red and blue) and the 1-68 region (colored in
green and red). c, backbone trace of GABARAP in the same
orientation as b, showing residues discussed in the text.
Conserved residues are shown in red for acidic residues, blue
for basic residues, magenta for polar residues, green for
residues involved in turns, and black for hydrophobic core
residues. The nonconserved Phe^3 is shown in light gray, and
water molecules involved in the region of the salt bridges are
shown in cyan. This figure was prepared with MOLSCRIPT (32) and
RASTER3D (33).
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Figure 4.
Fig. 4. Backbone traces of GABARAP structure (cyan)
superposed by yellow spheres indicating NH groups for residues
that experience chemical shift perturbations upon addition of
candidate peptide ligands I  V in A E,
respectively. Three different sphere sizes are used to indicate
the different classes of perturbation described in Table II:
large sphere, >1 linewidth; medium sphere, approximately 1
linewidth; and small sphere, <1 linewidth. F, space-filled
representation of the GABARAP structure colored according to the
surface electrostatic potential computed with the program GRASP
(25), with orientation identical to that in A E.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2002,
277,
5556-5561)
copyright 2002.
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