4TZ7

Crystal structure of type I phosphatidylinositol 4-phosphate 5-kinase alpha from Zebrafish


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Resolution of structure of PIP5K1A reveals molecular mechanism for its regulation by dimerization and dishevelled.

Hu, J.Yuan, Q.Kang, X.Qin, Y.Li, L.Ha, Y.Wu, D.

(2015) Nat Commun 6: 8205-8205

  • DOI: 10.1038/ncomms9205
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Type I phosphatidylinositol phosphate kinase (PIP5K1) phosphorylates the head group of phosphatidylinositol 4-phosphate (PtdIns4P) to generate PtdIns4,5P2, which plays important roles in a wide range of cellular functions including Wnt signalling. Ho ...

    Type I phosphatidylinositol phosphate kinase (PIP5K1) phosphorylates the head group of phosphatidylinositol 4-phosphate (PtdIns4P) to generate PtdIns4,5P2, which plays important roles in a wide range of cellular functions including Wnt signalling. However, the lack of its structural information has hindered the understanding of its regulation. Here we report the crystal structure of the catalytic domain of zebrafish PIP5K1A at 3.3 Å resolution. This molecule forms a side-to-side dimer. Mutagenesis study of PIP5K1A reveals two adjacent interfaces for the dimerization and interaction with the DIX domain of the Wnt signalling molecule dishevelled. Although these interfaces are located distally to the catalytic/substrate-binding site, binding to these interfaces either through dimerization or the interaction with DIX stimulates PIP5K1 catalytic activity. DIX binding additionally enhances PIP5K1 substrate binding. Thus, this study elucidates regulatory mechanisms for this lipid kinase and provides a paradigm for the understanding of PIP5K1 regulation by their interacting molecules.


    Organizational Affiliation

    Vascular Biology and Therapeutic Program, Yale School of Medicine, New Haven, Connecticut 06520 USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol-4-phosphate 5-kinase, type I, alphaA394Danio rerioMutation(s): 0 
Gene Names: pip5k1aapip5k1a
Find proteins for Q503I3 (Danio rerio)
Explore Q503I3 
Go to UniProtKB:  Q503I3
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.213 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.946α = 90
b = 88.946β = 90
c = 157.074γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2015-09-23
    Changes: Database references, Structure summary