4FIF

Catalytic domain of human PAK4 with RPKPLVDP peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

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Literature

Type II p21-activated kinases (PAKs) are regulated by an autoinhibitory pseudosubstrate.

Ha, B.H., Davis, M.J., Chen, C., Lou, H.J., Gao, J., Zhang, R., Krauthammer, M., Halaban, R., Schlessinger, J., Turk, B.E., Boggon, T.J.

(2012) Proc Natl Acad Sci U S A 109: 16107-16112

  • DOI: 10.1073/pnas.1214447109
  • Primary Citation of Related Structures:  
    4FIE, 4FIF, 4FIG, 4FIH, 4FII, 4FIJ

  • PubMed Abstract: 

    • The type II p21-activated kinases (PAKs) are key effectors of RHO-family GTPases involved in cell motility, survival, and proliferation. Using a structure-guided approach, we discovered that type II PAKs are regulated by an N-terminal autoinhibitory pseudosubstrate motif centered on a critical proline residue, and that this regulation occurs independently of activation loop phosphorylation ...

    The type II p21-activated kinases (PAKs) are key effectors of RHO-family GTPases involved in cell motility, survival, and proliferation. Using a structure-guided approach, we discovered that type II PAKs are regulated by an N-terminal autoinhibitory pseudosubstrate motif centered on a critical proline residue, and that this regulation occurs independently of activation loop phosphorylation. We determined six X-ray crystal structures of either full-length PAK4 or its catalytic domain, that demonstrate the molecular basis for pseudosubstrate binding to the active state with phosphorylated activation loop. We show that full-length PAK4 is constitutively autoinhibited, but mutation of the pseudosubstrate releases this inhibition and causes increased phosphorylation of the apoptotic regulation protein Bcl-2/Bcl-X(L) antagonist causing cell death and cellular morphological changes. We also find that PAK6 is regulated by the pseudosubstrate region, indicating a common type II PAK autoregulatory mechanism. Finally, we find Src SH3, but not β-PIX SH3, can activate PAK4. We provide a unique understanding for type II PAK regulation.

    Organizational Affiliation: 

    Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PAK 4A, B346Homo sapiensMutation(s): 0 
Gene Names: KIAA1142, PAK4
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O96013 (Homo sapiens)
Explore O96013 
Go to UniProtKB:  O96013
PHAROS:  O96013
GTEx:  ENSG00000130669 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO96013
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PAK 4C, D8Homo sapiensMutation(s): 0 
Gene Names: PAK4, KIAA1142
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O96013 (Homo sapiens)
Explore O96013 
Go to UniProtKB:  O96013
PHAROS:  O96013
GTEx:  ENSG00000130669 
Entity Groups  
UniProt GroupO96013
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]		PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP		A, B L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: P 3
  • Diffraction Data DOI: 10.15785/SBGRID/435 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.411α = 90
b = 141.411β = 90
c = 61.624γ = 120
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2012-06-08 
  • Released Date: 2012-09-12 
    • Deposition Author(s): Ha, B.H., Boggon, T.J.

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-12
    Type: Initial release
  • Version 1.1: 2012-09-26
    Changes: Database references
  • Version 1.2: 2012-10-31
    Changes: Database references