2IWL

Structure of the PX Domain of Phosphoinositide 3-Kinase-C2alpha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.252 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and Membrane Binding Analysis of the Phox Homology Domain of Phosphoinositide 3-Kinase- C2{Alpha}.

Stahelin, R.V.Karathanassis, D.Bruzik, K.S.Waterfield, M.D.Bravo, J.Williams, R.L.Cho, W.

(2006) J Biol Chem 281: 39396

  • DOI: 10.1074/jbc.M607079200
  • Primary Citation of Related Structures:  
    2IWL

  • PubMed Abstract: 
  • Phox homology (PX) domains, which have been identified in a variety of proteins involved in cell signaling and membrane trafficking, have been shown to interact with phosphoinositides (PIs) with different affinities and specificities. To elucidate the structural origin of diverse PI specificities of PX domains, we determined the crystal structure of the PX domain from phosphoinositide 3-kinase C2alpha (PI3K-C2alpha), which binds phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P(2)) ...

    Phox homology (PX) domains, which have been identified in a variety of proteins involved in cell signaling and membrane trafficking, have been shown to interact with phosphoinositides (PIs) with different affinities and specificities. To elucidate the structural origin of diverse PI specificities of PX domains, we determined the crystal structure of the PX domain from phosphoinositide 3-kinase C2alpha (PI3K-C2alpha), which binds phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P(2)). To delineate the mechanism by which this PX domain interacts with membranes, we measured the membrane binding of the wild type domain and mutants by surface plasmon resonance and monolayer techniques. This PX domain contains a signature PI-binding site that is optimized for PtdIns(4,5)P(2) binding. The membrane binding of the PX domain is initiated by nonspecific electrostatic interactions followed by the membrane penetration of hydrophobic residues. Membrane penetration is specifically enhanced by PtdIns(4,5)P(2). Furthermore, the PX domain displayed significantly higher PtdIns(4,5)P(2) membrane affinity and specificity when compared with the PI3K-C2alpha C2 domain, demonstrating that high affinity PtdIns(4,5)P(2) binding was facilitated by the PX domain in full-length PI3K-C2alpha. Together, these studies provide new structural insight into the diverse PI specificities of PX domains and elucidate the mechanism by which the PI3K-C2alpha PX domain interacts with PtdIns(4,5)P(2)-containing membranes and thereby mediates the membrane recruitment of PI3K-C2alpha.


    Organizational Affiliation

    Departments of Chemistry and Medicinal Chemistry and Pharmacognosy, University of Illinois, Chicago, Illinois 60607, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOSPHATIDYLINOSITOL-4-PHOSPHATE 3-KINASE C2 DOMAIN-CONTAINING ALPHA POLYPEPTIDEA [auth X]140Homo sapiensMutation(s): 0 
Gene Names: PIK3C2A
EC: 2.7.1.154 (PDB Primary Data), 2.7.1.137 (PDB Primary Data), 2.7.1.153 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O00443 (Homo sapiens)
Explore O00443 
Go to UniProtKB:  O00443
PHAROS:  O00443
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00443
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth X],
C [auth X],
D [auth X]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.252 
  • Space Group: P 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.933α = 90
b = 115.933β = 90
c = 115.933γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata scaling
autoSHARPphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Source and taxonomy