Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 91.67 kDa 
• Atom Count: 5273 
• Modelled Residue Count: 621 
• Deposited Residue Count: 786 
• Unique protein chains: 1

3X02

Crystal structure of PIP4KIIBETA complex with GMP

• DOI: 10.2210/pdb3X02/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-10-09 Released: 2015-10-14 
• Deposition Author(s): Takeuchi, K., Lo, Y.H., Sumita, K., Senda, M., Terakawa, J., Dimitoris, A., Locasale, J.W., Sasaki, M., Yoshino, H., Zhang, Y., Kahoud, E.R., Takano, T., Yokota, T., Emerling, B., Asara, J.A., Ishida, T., Shimada, I., Daikoku, T., Cantley, L.C., Senda, T., Sasaki, A.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.255 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 

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

• PubMed: 26774281 
• DOI: 10.1016/j.molcel.2015.12.011
• Primary Citation of Related Structures:  
  3X0C, 3X0A, 3X0B, 3X03, 3X04, 3X05, 3X06, 3X07, 3X08, 3X09


• 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 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.

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Organizational Affiliation: 

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: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 5-phosphate 4-kinase type-2 beta	A, B	393	Homo sapiens	Mutation(s): 0  Gene Names: PIP4K2B, PIP5K2B EC: 2.7.1.149
Find proteins for P78356 (Homo sapiens) Explore P78356  Go to UniProtKB:  P78356
NIH Common Fund Data Resources
PHAROS:  P78356 GTEx:  ENSG00000276293

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5GP	A, B	GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O8 P RQFCJASXJCIDSX-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.255 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.753	α = 90
b = 183.189	β = 90
c = 106.833	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-10-09 
• Released Date: 2015-10-14 
Deposition Author(s): Takeuchi, K., Lo, Y.H., Sumita, K., Senda, M., Terakawa, J., Dimitoris, A., Locasale, J.W., Sasaki, M., Yoshino, H., Zhang, Y., Kahoud, E.R., Takano, T., Yokota, T., Emerling, B., Asara, J.A., Ishida, T., Shimada, I., Daikoku, T., Cantley, L.C., Senda, T., Sasaki, A.T.

Revision History  

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