4PLA

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

• PDB DOI: https://doi.org/10.2210/pdb4PLA/pdb

• Classification: TRANSFERASE,HYDROLASE
• Organism(s): Homo sapiens, Tequatrovirus T4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMmpstruc


• Deposited: 2014-05-16 Released: 2014-09-10 
• Deposition Author(s): Baumlova, A., Chalupska, D., Boura, E.
• Funding Organization(s): MarieCurie FP7-PEOPLE-2012-CIG

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 0.251 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 

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

• PubMed: 25168678 
• DOI: https://doi.org/10.15252/embr.201438841
• Primary Citation of Related Structures:  
  4PLA


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.26 kDa 
• Atom Count: 3,951 
• Modelled Residue Count: 483 
• Deposited Residue Count: 556 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimera protein of Phosphatidylinositol 4-kinase type 2-alpha and Lysozyme	A	556	Homo sapiens, Tequatrovirus T4	Mutation(s): 2  Gene Names: PI4K2A, e, T4Tp126 EC: 2.7.1.67 (PDB Primary Data), 3.2.1.17 (PDB Primary Data) Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BTU6 (Homo sapiens) Explore Q9BTU6  Go to UniProtKB:  Q9BTU6
PHAROS:  Q9BTU6 GTEx:  ENSG00000155252
Find proteins for D9IEF7 (Enterobacteria phage T4) Explore D9IEF7  Go to UniProtKB:  D9IEF7
UniProt Groups	Q9BTU6D9IEF7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	B [auth A], C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 0.251 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.744	α = 90
b = 79.539	β = 90
c = 78.704	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-09-10 
Deposition Author(s): Baumlova, A., Chalupska, D., Boura, E.

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Funding Organization	Location	Grant Number
MarieCurie FP7-PEOPLE-2012-CIG		333916

Revision History  

• Version 1.0: 2014-09-10
  Type: Initial release
  
• Version 1.1: 2014-10-15
  Changes: Database references
• Version 1.2: 2015-02-04
  Changes: Derived calculations
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy