4HNE

Crystal structure of the catalytic domain of human type II alpha Phosphatidylinositol 4-kinase (PI4KIIalpha) in complex with ADP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

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Literature

Molecular insights into the membrane-associated phosphatidylinositol 4-kinase II alpha.

Zhou, Q., Li, J., Yu, H., Zhai, Y., Gao, Z., Liu, Y., Pang, X., Zhang, L., Schulten, K., Sun, F., Chen, C.

(2014) Nat Commun 5: 3552-3552

  • DOI: 10.1038/ncomms4552
  • Primary Citation of Related Structures:  
    4HND, 4HNE

  • PubMed Abstract: 

    • Phosphatidylinositol 4-kinase IIα (PI4KIIα), a membrane-associated PI kinase, plays a central role in cell signalling and trafficking. Its kinase activity critically depends on palmitoylation of its cysteine-rich motif (-CCPCC-) and is modulated by the membrane environment ...

    Phosphatidylinositol 4-kinase IIα (PI4KIIα), a membrane-associated PI kinase, plays a central role in cell signalling and trafficking. Its kinase activity critically depends on palmitoylation of its cysteine-rich motif (-CCPCC-) and is modulated by the membrane environment. Lack of atomic structure impairs our understanding of the mechanism regulating kinase activity. Here we present the crystal structure of human PI4KIIα in ADP-bound form. The structure identifies the nucleotide-binding pocket that differs notably from that found in PI3Ks. Two structural insertions, a palmitoylation insertion and an RK-rich insertion, endow PI4KIIα with the 'integral' membrane-binding feature. Molecular dynamics simulations, biochemical and mutagenesis studies reveal that the palmitoylation insertion, containing an amphipathic helix, contributes to the PI-binding pocket and anchors PI4KIIα to the membrane, suggesting that fluctuation of the palmitoylation insertion affects PI4KIIα's activity. We conclude from our results that PI4KIIα's activity is regulated indirectly through changes in the membrane environment.

    Organizational Affiliation: 

    1] National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China [2] Beijing Institute for Brain Disorders, Beijing 100069, China.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidylinositol 4-kinase type 2-alphaA, B384Homo sapiensMutation(s): 4 
Gene Names: PI4K2A, PI4KIIA (AMINO ACIDS 78-453)
EC: 2.7.1.67
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BTU6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ADP BindingDB:  4HNE Ki: 1.00e+5 (nM) from 1 assay(s)
IC50: 1.45e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 191.824α = 90
b = 191.824β = 90
c = 157.543γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-09
    Type: Initial release