4A55

Crystal structure of p110alpha in complex with iSH2 of p85alpha and the inhibitor PIK-108


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Regulation of Lipid Binding Underlies the Activation Mechanism of Class Ia Pi3-Kinases.

Hon, W.-C.Berndt, A.Williams, R.L.

(2012) Oncogene 31: 3655

  • DOI: 10.1038/onc.2011.532

  • PubMed Abstract: 
  • Somatic missense mutations in PIK3CA, which encodes the p110α catalytic subunit of phosphoinositide 3-kinases, occur frequently in human cancers. Activating mutations spread across multiple domains, some of which are located at inhibitory contact sit ...

    Somatic missense mutations in PIK3CA, which encodes the p110α catalytic subunit of phosphoinositide 3-kinases, occur frequently in human cancers. Activating mutations spread across multiple domains, some of which are located at inhibitory contact sites formed with the regulatory subunit p85α. PIK3R1, which encodes p85α, also has activating somatic mutations. We find a strong correlation between lipid kinase and lipid-binding activities for both wild-type (WT) and a representative set of oncogenic mutant complexes of p110α/p85α. Lipid binding involves both electrostatic and hydrophobic interactions. Activation caused by a phosphorylated receptor tyrosine kinase (RTK) peptide binding to the p85α N-terminal SH2 domain (nSH2) induces lipid binding. This depends on the polybasic activation loop as well as a conserved hydrophobic motif in the C-terminal region of the kinase domain. The hotspot E545K mutant largely mimics the activated WT p110α. It shows the highest basal activity and lipid binding, and is not significantly activated by an RTK phosphopeptide. Both the hotspot H1047R mutant and rare mutations (C420R, M1043I, H1047L, G1049R and p85α-N564D) also show increased basal kinase activities and lipid binding. However, their activities are further enhanced by an RTK phosphopeptide to levels markedly exceeding that of activated WT p110α. Phosphopeptide binding to p110β/p85α and p110δ/p85α complexes also induces their lipid binding. We present a crystal structure of WT p110α complexed with the p85α inter-SH2 domain and the inhibitor PIK-108. Additional to the ATP-binding pocket, an unexpected, second PIK-108 binding site is observed in the kinase C-lobe. We show a global conformational change in p110α consistent with allosteric regulation of the kinase domain by nSH2. These findings broaden our understanding of the differential biological outputs exhibited by distinct types of mutations regarding growth factor dependence, and suggest a two-tier classification scheme relating p110α and p85α mutations with signalling potential.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT ALPHA ISOFORM
A
1096Mus musculusMutation(s): 0 
Gene Names: Pik3ca
EC: 2.7.1.153
Find proteins for P42337 (Mus musculus)
Go to UniProtKB:  P42337
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY SUBUNIT ALPHA
B
279Homo sapiensMutation(s): 0 
Gene Names: PIK3R1 (GRB1)
Find proteins for P27986 (Homo sapiens)
Go to Gene View: PIK3R1
Go to UniProtKB:  P27986
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P08
Query on P08

Download SDF File 
Download CCD File 
A
PIK-108
C22 H24 N2 O3
VRCXIJAYLCUSHC-INIZCTEOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
P08IC50: >10000 nM (98) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.183 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 136.092α = 90.00
b = 147.184β = 90.00
c = 226.478γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2012-08-29
    Type: Database references