4PLA

Crystal structure of phosphatidyl inositol 4-kinase II alpha in complex with ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.771 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of the phosphatidylinositol 4-kinase II alpha.

Baumlova, A.Chalupska, D.Rozycki, B.Jovic, M.Wisniewski, E.Klima, M.Dubankova, A.Kloer, D.P.Nencka, R.Balla, T.Boura, E.

(2014) Embo Rep. 15: 1085-1092

  • DOI: 10.15252/embr.201438841

  • PubMed Abstract: 
  • Phosphoinositides are a class of phospholipids generated by the action of phosphoinositide kinases with key regulatory functions in eukaryotic cells. Here, we present the atomic structure of phosphatidylinositol 4-kinase type IIα (PI4K IIα), in compl ...

    Phosphoinositides are a class of phospholipids generated by the action of phosphoinositide kinases with key regulatory functions in eukaryotic cells. Here, we present the atomic structure of phosphatidylinositol 4-kinase type IIα (PI4K IIα), in complex with ATP solved by X-ray crystallography at 2.8 Å resolution. The structure revealed a non-typical kinase fold that could be divided into N- and C-lobes with the ATP binding groove located in between. Surprisingly, a second ATP was found in a lateral hydrophobic pocket of the C-lobe. Molecular simulations and mutagenesis analysis revealed the membrane binding mode and the putative function of the hydrophobic pocket. Taken together, our results suggest a mechanism of PI4K IIα recruitment, regulation, and function at the membrane.


    Organizational Affiliation

    Institute of Organic Chemistry and Biochemistry AS CR, Prague, Czech Republic.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chimera protein of Phosphatidylinositol 4-kinase type 2-alpha and Lysozyme
A
556Homo sapiensEnterobacteria phage T4
This entity is chimeric
Mutation(s): 2 
Gene Names: PI4K2A, e
EC: 2.7.1.67 3.2.1.17
Membrane protein
mpstruct
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Phosphoinositide Kinases
Protein: 
Phosphatidylinositol 4-kinase IIα
Find proteins for Q9BTU6 (Homo sapiens)
Go to Gene View: PI4K2A
Go to UniProtKB:  Q9BTU6
Find proteins for D9IEF7 (Enterobacteria phage T4)
Go to UniProtKB:  D9IEF7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.771 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.211 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 104.744α = 90.00
b = 79.539β = 90.00
c = 78.704γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MarieCurie FP7-PEOPLE-2012-CIG333916

Revision History 

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2014-10-15
    Type: Database references
  • Version 1.2: 2015-02-04
    Type: Derived calculations