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PDBsum entry 2gnc
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Signaling protein
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PDB id
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2gnc
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References listed in PDB file
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Key reference
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Title
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Structural basis of robo proline-Rich motif recognition by the srgap1 src homology 3 domain in the slit-Robo signaling pathway.
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Authors
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X.Li,
Y.Chen,
Y.Liu,
J.Gao,
F.Gao,
M.Bartlam,
J.Y.Wu,
Z.Rao.
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Ref.
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J Biol Chem, 2006,
281,
28430-28437.
[DOI no: ]
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PubMed id
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Abstract
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The Slit-Robo (sr) GTPase-activating protein (GAPs) are important components in
the intracellular pathway mediating Slit-Robo signaling in axon guidance and
cell migration. We report the first crystal structure of the srGAP1 SH3 domain
at 1.8-A resolution. The unusual side chain conformation of the conserved Phe-13
in the P1 pocket renders the ligand binding pocket shallow and narrow, which
contributes toward the low binding affinity. Moreover, the opposing
electrostatic charge and the hydrophobic properties of the P3 specificity pocket
are consistent with the observed binding characteristics of the srGAP1 SH3
domain to its ligand. Surface plasmon resonance experiments indicate that the
srGAP1 SH3 domain interacts with its natural ligand inaCtoN orientation. The
srGAP1 SH3 domain can bind to both the CC2 and CC3 motifs in vitro. The
N-terminal two acidic residues in the CC3 motif recognition site are necessary
for srGAP1 SH3 domain binding. A longer CC3 peptide (CC3-FL) binds with greater
affinity than its shorter counterpart, suggesting that the residues surrounding
the proline-rich core are important for protein-peptide interactions. Our study
reveals previously unknown properties of the srGAP-Robo interaction. Our data
provide a structural basis for the srGAP-Robo interaction, consistent with the
role of the Robo intracellular domain in interacting with other downstream
signaling molecules and mediating versatile and dynamic responses to axon
guidance and cell migration cues.
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Figure 3.
FIGURE 3. Stereo view showing a comparison of the srGAP1
SH3 domain with other SH3 domain structures. The residues
forming the ligand binding pockets are shown in ball-and-stick
representations. Molecule A of the srGAP1 SH3 domain is colored
blue and molecule B is colored spring green, the  -spectrin SH3 domain
(PDB code 1BK2) (24) is colored gold, the Crk-N SH3 domain (PDB
code 1CKA) (28) is colored brown, and the Abl tyrosine kinase
SH3 domain (PDB code 1ABO) (29) is colored magenta. Residues are
labeled corresponding to their positions in the srGAP1 SH3
domain.
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Figure 5.
FIGURE 5. Surface representations of the SH3 domains from
Crk-N complexed with C3G peptide, Abl complex with 3BP1, and
srGAP1. The views on the left depict surface accessible
hydrophobic regions colored in yellow. On the right are
representations of electrostatic potential showing the peptide
binding surface of the SH3 domains with the n-Src loops pointing
toward the top, in which the positive electrostatic potential is
colored in blue, negative electrostatic potential is colored in
red, and hydrophobic surface is colored white. Peptides are in
ball-and-stick representation. Coordinates for the SH3 domains
of Crk-N and Abl were obtained from the Protein Data Bank. In
the surface of the SH3 domain of srGAP1, the red circles
indicate the four pockets in the ligand binding groove. The
figure was produced by CCP4mg and PyMOL.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2006,
281,
28430-28437)
copyright 2006.
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