6WLY

PAK4 kinase domain in complex with LIMK1 Thr508 substrate peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Recognition of physiological phosphorylation sites by p21-activated kinase 4.

Chetty, A.K.Sexton, J.A.Hak Ha, B.Turk, B.E.Boggon, T.J.

(2020) J Struct Biol : 107553-107553

  • DOI: 10.1016/j.jsb.2020.107553
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Many serine/threonine protein kinases discriminate between serine and threonine substrates as a filter to control signaling output. Among these, the p21-activated kinase (PAK) group strongly favors phosphorylation of Ser over Thr residues. PAK4, a gr ...

    Many serine/threonine protein kinases discriminate between serine and threonine substrates as a filter to control signaling output. Among these, the p21-activated kinase (PAK) group strongly favors phosphorylation of Ser over Thr residues. PAK4, a group II PAK, almost exclusively phosphorylates its substrates on serine residues. The only well documented exception is LIM domain kinase 1 (LIMK1), which is phosphorylated on an activation loop threonine (Thr508) to promote its catalytic activity. To understand the molecular and kinetic basis for PAK4 substrate selectivity we compared its mode of recognition of LIMK1 (Thr508) with that of a known serine substrate, β-catenin (Ser675). We determined X-ray crystal structures of PAK4 in complex with synthetic peptides corresponding to its phosphorylation sites in LIMK1 and β-catenin to 1.9 Å and 2.2 Å resolution, respectively. We found that the PAK4 DFG+1 residue, a key determinant of phosphoacceptor preference, adopts a sub-optimal orientation when bound to LIMK1 compared to β-catenin. In peptide kinase activity assays, we find that phosphoacceptor identity impacts catalytic efficiency but does not affect the K m value for both phosphorylation sites. Although catalytic efficiency of wild-type LIMK1 and β-catenin are equivalent, T508S mutation of LIMK1 creates a highly efficient substrate. These results suggest suboptimal phosphorylation of LIMK1 as a mechanism for controlling the dynamics of substrate phosphorylation by PAK4.


    Organizational Affiliation

    Molecular Biophysics and Biochemistry, 333 Cedar Street, New Haven, CT, 06520, USA; Pharmacology and the Yale Cancer Center, Yale University, 333 Cedar Street, New Haven, CT, 06520, USA; Yale Cancer Center, Yale University, 333 Cedar Street, New Haven, CT, 06520, USA. Electronic address: titus.boggon@yale.edu.



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: PAK4KIAA1142
EC: 2.7.11.1
Find proteins for O96013 (Homo sapiens)
Go to UniProtKB:  O96013
NIH Common Fund Data Resources
PHAROS  O96013
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LIM Kinase 1 peptide
B
10Homo sapiensMutation(s): 0 
Gene Names: LIMK1LIMK
EC: 2.7.11.1
Find proteins for P53667 (Homo sapiens)
Go to UniProtKB:  P53667
NIH Common Fund Data Resources
PHAROS  P53667
Protein Feature View
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 41 21 2
  • Diffraction Data DOI: 10.15785/SBGRID/782 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.626α = 90
b = 61.626β = 90
c = 179.596γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM102262
American Heart AssociationUnited States19IPLOI34740007

Revision History 

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references