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PDBsum entry 2g6f
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Signaling protein
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PDB id
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2g6f
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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 sh3 domain of betapix in complex with a high affinity peptide from pak2.
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Authors
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A.Hoelz,
J.M.Janz,
S.D.Lawrie,
B.Corwin,
A.Lee,
T.P.Sakmar.
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Ref.
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J Mol Biol, 2006,
358,
509-522.
[DOI no: ]
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PubMed id
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Abstract
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The p21-activated kinases (PAKs) are important effector proteins of the small
GTPases Cdc42 and Rac and control cytoskeletal rearrangements and cell
proliferation. The direct interaction of PAKs with guanine nucleotide exchange
factors from the PIX/Cool family, which is responsible for the localization of
PAK kinases to focal complexes in the cell, is mediated by a 24-residue peptide
segment in PAKs and an N-terminal src homology 3 (SH3) domain in PIX/Cool. The
SH3-binding segment of PAK contains the atypical consensus-binding motif PxxxPR,
which is required for unusually high affinity binding. In order to understand
the structural basis for the high affinity and specificity of the PIX-PAK
interaction, we solved crystal structures for the N-terminal SH3 domain of
betaPIX and for the complex of the atypical binding segment of PAK2 with the
N-terminal SH3 domain of betaPIX at 0.92 A and 1.3A resolution, respectively.
The asymmetric unit of the crystal contains two SH3 domains and two peptide
ligands. The bound peptide adopts a conformation that allows for intimate
contacts with three grooves on the surface of the SH3 domain that lie between
the n-Src and RT-loops. Most notably, the arginine residue of the PxxxPR motif
forms a salt-bridge and is tightly coordinated by a number of residues in the
SH3 domain. This arginine-specific interaction appears to be the key determinant
for the high affinity binding of PAK peptides. Furthermore, C-terminal residues
of the peptide engage in additional interactions with the surface of the
RT-loop, which significantly increases binding specificity. Compared to a recent
NMR structure of a similar complex, our crystal structure reveals an alternate
binding mode. Finally, we compare our crystal structure with the recently
published betaPIX/Cbl-b complex structure, and suggest the existence of a
molecular switch.
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Figure 4.
Figure 4. The interface between the bPIX-SH3 domain and the
PAK2-derived peptide. (a) Stereo view of the structure of the
bPIX-SH3/PAK2 complex (red and yellow) which is superimposed on
the structure of the bPIX-SH3 domain (gray). (b) The
simulated-annealed 2F[o] -F[c] electron density map, sliced at
2.5 s, is shown for the PAK peptide (yellow stick
representation). The C^a trace of the bPIX-SH3 domain is shown
in red below the transparent van der Waals representation of the
surface (gray). (c) Close-up view of the entire interface. PAK2
residues are labeled in yellow, and bPIX-SH3 domain residues are
labeled in red. Residues in PAK2 that are essential for the
interaction are labeled in orange.
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Figure 6.
Figure 6. Comparison of the bPIX-SH3/PAK2 structure to
other bPIX-SH3 structures. (a) Superposition of the crystal and
NMR structures of the bPIX-SH3/PAK complex. Peptides are
illustrated in stick representation. The bPIX-SH3 surface is
shown in gray, and the peptides are colored according to the
legend in (a). (b) Structure of the bPIX-SH3/Cbl-b complex shown
in ribbon representation (PDB code 2AK5). The two bPIX-SH3
domains and the Cbl-b peptide are colored according to the
legend in (b). (c) Superposition of the bPIX-SH3/PAK2 crystal
structure with the bPIX-SH3 B/Cbl-b crystal structure. bPIX-SH3
A has been removed for clarity. Peptides are illustrated in
stick representation. The peptides of the crystal structures are
colored according to the legend in (c).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2006,
358,
509-522)
copyright 2006.
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