4JDI

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.192 

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:  

  • 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 thr ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase PAK 4
A
346Homo sapiensMutation(s): 0 
Gene Names: PAK4 (KIAA1142)
EC: 2.7.11.1
Find proteins for O96013 (Homo sapiens)
Go to Gene View: PAK4
Go to UniProtKB:  O96013
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Paktide S
B
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 61.912α = 90.00
b = 61.912β = 90.00
c = 181.560γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Executordata collection
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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