2DF6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

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Literature

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

Hoelz, A.Janz, J.M.Lawrie, S.D.Corwin, B.Lee, A.Sakmar, T.P.

(2006) J Mol Biol 358: 509-522

  • DOI: 10.1016/j.jmb.2006.02.027
  • Primary Citation of Related Structures:  
    2G6F, 2DF6

  • PubMed Abstract: 
  • 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 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.


    Organizational Affiliation

    The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA. hoelza@rockefeller.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Rho guanine nucleotide exchange factor 7A, B59Rattus norvegicusMutation(s): 0 
Gene Names: Arhgef7Pak3bpPixb
UniProt
Find proteins for O55043 (Rattus norvegicus)
Explore O55043 
Go to UniProtKB:  O55043
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
18-mer from PAK2C, D18N/AMutation(s): 0 
EC: 2.7.1.37
UniProt
Find proteins for Q64303 (Rattus norvegicus)
Explore Q64303 
Go to UniProtKB:  Q64303
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.217α = 90
b = 50.217β = 90
c = 100.317γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2006-02-25 
  • Released Date: 2006-04-11 
  • Deposition Author(s): Hoelz, A.

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance