6FJK

Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with myo-IP6 and ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.025 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Fluorescent Probe Identifies Active Site Ligands of Inositol Pentakisphosphate 2-Kinase.

Whitfield, H.Gilmartin, M.Baker, K.Riley, A.M.Godage, H.Y.Potter, B.V.L.Hemmings, A.M.Brearley, C.A.

(2018) J. Med. Chem. 61: 8838-8846

  • DOI: 10.1021/acs.jmedchem.8b01022
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Inositol pentakisphosphate 2-kinase catalyzes the phosphorylation of the axial 2-OH of myo-inositol 1,3,4,5,6-pentakisphosphate for de novo synthesis of myo-inositol hexakisphosphate. Disruption of inositol pentakisphosphate 2-kinase profoundly influ ...

    Inositol pentakisphosphate 2-kinase catalyzes the phosphorylation of the axial 2-OH of myo-inositol 1,3,4,5,6-pentakisphosphate for de novo synthesis of myo-inositol hexakisphosphate. Disruption of inositol pentakisphosphate 2-kinase profoundly influences cellular processes, from nuclear mRNA export and phosphate homeostasis in yeast and plants to establishment of left-right asymmetry in zebrafish. We elaborate an active site fluorescent probe that allows high throughput screening of Arabidopsis inositol pentakisphosphate 2-kinase. We show that the probe has a binding constant comparable to the K m values of inositol phosphate substrates of this enzyme and can be used to prospect for novel substrates and inhibitors of inositol phosphate kinases. We identify several micromolar K i inhibitors and validate this approach by solving the crystal structure of protein in complex with purpurogallin. We additionally solve structures of protein in complexes with epimeric higher inositol phosphates. This probe may find utility in characterization of a wide family of inositol phosphate kinases.


    Organizational Affiliation

    Medicinal Chemistry & Drug Discovery, Department of Pharmacology , University of Oxford , Mansfield Road , Oxford OX1 3QT , U.K.,School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , U.K.,Medicinal Chemistry, Department of Pharmacy and Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inositol-pentakisphosphate 2-kinase
A, B
470Arabidopsis thalianaMutation(s): 0 
Gene Names: IPK1
EC: 2.7.1.158
Find proteins for Q93YN9 (Arabidopsis thaliana)
Go to UniProtKB:  Q93YN9
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I6P
Query on I6P

Download SDF File 
Download CCD File 
A, B
INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE
MYO-INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP

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Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

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Download CCD File 
B
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.025 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.178 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 59.810α = 88.53
b = 60.340β = 89.18
c = 83.980γ = 63.36
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
xia2data reduction
xia2data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-09-12
    Type: Initial release
  • Version 1.1: 2018-10-31
    Type: Data collection, Database references
  • Version 1.2: 2019-06-12
    Type: Data collection, Structure summary