3X09

Crystal structure of PIP4KIIBETA F205L complex with AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.203 

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

    Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA.,Department of Pharmacology and Cancer Biology, Duke Cancer Institute and Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Cancer Metabolism Laboratory, The Francis Crick Institute, London NW7 1AA, UK.,Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Chemistry, Biology & Marine Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan.,Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.,Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Department of Cancer Biology and Department of Neurosurgery, University of Cincinnati College of Medicine, Brain Tumor Center at University of Cincinnati Neuroscience Institute, Cincinnati, OH 45267, USA. Electronic address: atsuo.sasaki@uc.edu.,Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA.,Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan.,Department of Neurology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA.,Biomedicinal Information Research Center and Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Koto, Tokyo 135-0064, Japan.,Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan; Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University of Advanced Studies (Soken-dai), Tsukuba, Ibaraki 305-0801, Japan. Electronic address: toshiya.senda@kek.jp.




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: 2.7 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.203 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 108.271α = 90.00
b = 183.424β = 90.00
c = 107.275γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
XDSdata reduction
PHASERphasing
PHENIXrefinement
XSCALEdata scaling

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