6E7F

Crystal Structure of Human Inositol Polyphosphate Multikinase (IPMK) Catalytic Core Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystallographic and kinetic analyses of human IPMK reveal disordered domains modulate ATP binding and kinase activity.

Seacrist, C.D.Blind, R.D.

(2018) Sci Rep 8: 16672-16672

  • DOI: 10.1038/s41598-018-34941-3
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Inositol polyphosphate multikinase (IPMK) is a member of the IPK-superfamily of kinases, catalyzing phosphorylation of several soluble inositols and the signaling phospholipid PI(4,5)P <sub>2 </sub> (PIP <sub>2 </sub>). IPMK also has critical non-cat ...

    Inositol polyphosphate multikinase (IPMK) is a member of the IPK-superfamily of kinases, catalyzing phosphorylation of several soluble inositols and the signaling phospholipid PI(4,5)P 2 (PIP 2 ). IPMK also has critical non-catalytic roles in p53, mTOR/Raptor, TRAF6 and AMPK signaling mediated partly by two disordered domains. Although IPMK non-catalytic functions are well established, it is less clear if the disordered domains are important for IPMK kinase activity or ATP binding. Here, kinetic and structural analyses of an engineered human IPMK lacking all disordered domains (ΔIPMK) are presented. Although the K M for PIP 2 is identical between ΔIPMK and wild type, ΔIPMK has a 1.8-fold increase in k cat for PIP 2 , indicating the native IPMK disordered domains decrease IPMK activity in vitro. The 2.5 Å crystal structure of ΔIPMK is reported, confirming the conserved ATP-grasp fold. A comparison with other IPK-superfamily structures revealed a putative "ATP-clamp" in the disordered N-terminus, we predicted would stabilize ATP binding. Consistent with this observation, removal of the ATP clamp sequence increases the K M for ATP 4.9-fold, indicating the N-terminus enhances ATP binding to IPMK. Together, these structural and kinetic studies suggest in addition to mediating protein-protein interactions, the disordered domains of IPMK impart modulatory capacity to IPMK kinase activity through multiple kinetic mechanisms.


    Organizational Affiliation

    Departments of Pharmacology, Biochemistry and Medicine; Division of Diabetes, Endocrinology and Metabolism, Vanderbilt Diabetes Research and Training Center, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA. ray.blind@vanderbilt.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inositol polyphosphate multikinase
A, B
278Homo sapiensMutation(s): 0 
Gene Names: IPMKIMPK
EC: 2.7.1.151 (PDB Primary Data), 2.7.1.140 (UniProt), 2.7.1.153 (UniProt)
Find proteins for Q8NFU5 (Homo sapiens)
Go to UniProtKB:  Q8NFU5
NIH Common Fund Data Resources
PHAROS  Q8NFU5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.66α = 90
b = 109.36β = 90
c = 73.6γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
BALBESphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-07-26 
  • Released Date: 2018-11-07 
  • Deposition Author(s): Blind, R., Seacrist, C.
  • This entry supersedes: 6C8A

Funding OrganizationLocationGrant Number
American Cancer SocietyUnited StatesRSG-17-063-01
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesK01 CA172957

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence