4L67

Crystal Structure of Catalytic Domain of PAK4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

NMR binding and crystal structure reveal that intrinsically-unstructured regulatory domain auto-inhibits PAK4 by a mechanism different for that of PAK1

Wang, W.Lim, L.Baskaran, Y.Manser, E.Song, J.

(2013) Biochem.Biophys.Res.Commun. 438: 169-174

  • DOI: 10.1016/j.bbrc.2013.07.047

  • PubMed Abstract: 
  • Six human PAK members are classified into groups I (PAKs 1-3) and II (PAK4-6). Previously, only group I PAKs were thought to be auto-inhibited but very recently PAK4, the prototype of group II PAKs, has also been shown to be auto-inhibited by its N-t ...

    Six human PAK members are classified into groups I (PAKs 1-3) and II (PAK4-6). Previously, only group I PAKs were thought to be auto-inhibited but very recently PAK4, the prototype of group II PAKs, has also been shown to be auto-inhibited by its N-terminal regulatory domain. However, the complete auto-inhibitory domain (AID) sequence remains undefined and the mechanism underlying its auto-inhibition is largely elusive. Here, the N-terminal regulatory domain of PAK4 sufficient for auto-inhibiting and binding Cdc42/Rac was characterized to be intrinsically unstructured, but nevertheless we identified the entire AID sequence by NMR. Strikingly, an AID peptide was derived by deleting the binding-unnecessary residues, which has a Kd of 320 nM to the PAK4 catalytic domain. Consequently, the PAK4 crystal structure complexed with the entire AID has been determined, which reveals that the complete kinase cleft is occupied by 20 AID residuescomposed of an N-terminal α-helix and a previously-identified pseudosubstrate motif, thus achieving auto-inhibition. Our study reveals that PAK4 is auto-inhibited by a novel mechanism which is completely different from that for PAK1, thus bearing critical implications for design of inhibitors specific for group II PAKs.


    Organizational Affiliation

    Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase PAK 4
A
292Homo 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
Serine/threonine-protein kinase PAK 4
B
25Homo 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
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.228 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 65.175α = 90.00
b = 65.175β = 90.00
c = 184.567γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
HKL-2000data reduction
CCP4model building
HKL-2000data scaling
CCP4phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-06-12 
  • Released Date: 2013-08-14 
  • Deposition Author(s): Wang, W., Song, J.

Revision History 

  • Version 1.0: 2013-08-14
    Type: Initial release
  • Version 1.1: 2013-09-04
    Type: Database references