4PLA | pdb_00004pla

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 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

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 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.
Institute of Physics Polish Academy of Sciences, Warsaw, Poland.
Section on Molecular Signal Transduction, Program for Developmental Neuroscience, NICHD NIH, Bethesda, MD, USA.
Syngenta Jealott's Hill Internation Research Centre, Bracknell, UK.
Institute of Organic Chemistry and Biochemistry AS CR, Prague, Czech Republic [e-mail].

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 
• Modeled 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 D9IEF7 (Enterobacteria phage T4) Explore D9IEF7  Go to UniProtKB:  D9IEF7
Find proteins for Q9BTU6 (Homo sapiens) Explore Q9BTU6  Go to UniProtKB:  Q9BTU6
PHAROS:  Q9BTU6 GTEx:  ENSG00000155252
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 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

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