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Published April 28, 2006 | public
Journal Article

Crystal Structure of the SH3 Domain of βPIX in Complex with a High Affinity Peptide from PAK2


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 βPIX and for the complex of the atypical binding segment of PAK2 with the N-terminal SH3 domain of βPIX at 0.92 Å and 1.3 Å 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 βPIX/Cbl-b complex structure, and suggest the existence of a molecular switch.

Additional Information

© 2006 Elsevier Ltd. Received 29 November 2005, Revised 8 February 2006, Accepted 9 February 2006, Available online 28 February 2006. The authors thank Louis Lim for a kind gift of rat βPIX cDNA, John Kuriyan, in whose laboratory this project was started, Günter Blobel for support and advice, Jonathan Chernoff, Holger Sondermann, Thomas Schwarz, Alina Patke and Bushan Nagar for stimulating discussions, the members of the Blobel laboratory for comments on the manuscript, Udupi A. Ramagopal for his excellent scientific support and help with X-ray measurements at beamline X9A, National Synchrotron Light Source (NSLS) at the Brookhaven National Laboratory (BNL), Stephanie Etherton for help with editing of the manuscript, and Helen Mott for sharing data prior to publication. A.H. was supported by a pre-doctoral fellowship from the Burroughs Wellcome Fund Interfaces in Science program and by a post-doctoral fellowship from the Murray Foundation. J.M.J. was supported by NIH grant T3ZEY007138. B.C. was supported by HHMI as a summer research student.

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