4JDK

Crystal structure of Serine/threonine-protein kinase PAK 4 F461V mutant in complex with Paktide S peptide substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Identification of a major determinant for serine-threonine kinase phosphoacceptor specificity.

Chen, C.Ha, B.H.Thevenin, A.F.Lou, H.J.Zhang, R.Yip, K.Y.Peterson, J.R.Gerstein, M.Kim, P.M.Filippakopoulos, P.Knapp, S.Boggon, T.J.Turk, B.E.

(2014) Mol Cell 53: 140-147

  • DOI: 10.1016/j.molcel.2013.11.013
  • Primary Citation of Related Structures:  
    4JDH, 4JDI, 4JDJ, 4JDK

  • PubMed Abstract: 
  • Eukaryotic protein kinases are generally classified as being either tyrosine or serine-threonine specific. Though not evident from inspection of their primary sequences, many serine-threonine kinases display a significant preference for serine or threonine as the phosphoacceptor residue ...

    Eukaryotic protein kinases are generally classified as being either tyrosine or serine-threonine specific. Though not evident from inspection of their primary sequences, many serine-threonine kinases display a significant preference for serine or threonine as the phosphoacceptor residue. Here we show that a residue located in the kinase activation segment, which we term the "DFG+1" residue, acts as a major determinant for serine-threonine phosphorylation site specificity. Mutation of this residue was sufficient to switch the phosphorylation site preference for multiple kinases, including the serine-specific kinase PAK4 and the threonine-specific kinase MST4. Kinetic analysis of peptide substrate phosphorylation and crystal structures of PAK4-peptide complexes suggested that phosphoacceptor residue preference is not mediated by stronger binding of the favored substrate. Rather, favored kinase-phosphoacceptor combinations likely promote a conformation optimal for catalysis. Understanding the rules governing kinase phosphoacceptor preference allows kinases to be classified as serine or threonine specific based on their sequence.


    Organizational Affiliation

    Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA. Electronic address: ben.turk@yale.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PAK 4A346Homo sapiensMutation(s): 1 
Gene Names: KIAA1142PAK4
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

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Paktide SB7N/AMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 41 21 2
  • Diffraction Data DOI: 10.15785/SBGRID/441 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.621α = 90
b = 61.621β = 90
c = 180.757γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2013-02-25 
  • Released Date: 2014-01-29 
  • Deposition Author(s): Ha, B.H., Boggon, T.J.

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-29
    Type: Initial release