3X0B

Crystal structure of PIP4KIIBETA I368A complex with AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Lipid Kinase PI5P4K beta Is an Intracellular GTP Sensor for Metabolism and Tumorigenesis

Sumita, K.Lo, Y.H.Takeuchi, K.Senda, M.Kofuji, S.Ikeda, Y.Terakawa, J.Sasaki, M.Yoshino, H.Majd, N.Zheng, Y.Kahoud, E.R.Yokota, T.Emerling, B.M.Asara, J.M.Ishida, T.Locasale, J.W.Daikoku, T.Anastasiou, D.Senda, T.Sasaki, A.T.

(2016) Mol.Cell 61: 187-198

  • DOI: 10.1016/j.molcel.2015.12.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • While cellular GTP concentration dramatically changes in response to an organism's cellular status, whether it serves as a metabolic cue for biological signaling remains elusive due to the lack of molecular identification of GTP sensors. Here we repo ...

    While cellular GTP concentration dramatically changes in response to an organism's cellular status, whether it serves as a metabolic cue for biological signaling remains elusive due to the lack of molecular identification of GTP sensors. Here we report that PI5P4Kβ, a phosphoinositide kinase that regulates PI(5)P levels, detects GTP concentration and converts them into lipid second messenger signaling. Biochemical analyses show that PI5P4Kβ preferentially utilizes GTP, rather than ATP, for PI(5)P phosphorylation, and its activity reflects changes in direct proportion to the physiological GTP concentration. Structural and biological analyses reveal that the GTP-sensing activity of PI5P4Kβ is critical for metabolic adaptation and tumorigenesis. These results demonstrate that PI5P4Kβ is the missing GTP sensor and that GTP concentration functions as a metabolic cue via PI5P4Kβ. The critical role of the GTP-sensing activity of PI5P4Kβ in cancer signifies this lipid kinase as a cancer therapeutic target.


    Organizational Affiliation

    Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 5-phosphate 4-kinase type-2 beta
A, B
393Homo sapiensMutation(s): 1 
Gene Names: PIP4K2B (PIP5K2B)
EC: 2.7.1.149
Find proteins for P78356 (Homo sapiens)
Go to Gene View: PIP4K2B
Go to UniProtKB:  P78356
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download SDF File 
Download CCD File 
A, B
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.253 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 108.583α = 90.00
b = 182.143β = 90.00
c = 107.198γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2016-02-03
    Type: Database references