RCSB PDB - 8PPA: Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with D-myo-inositol 1,4,6-trisphosphate/AMP-PNP/Mn

 8PPA

Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with D-myo-inositol 1,4,6-trisphosphate/AMP-PNP/Mn


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ANPClick on this verticalbar to view detailsBest fitted 06GClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Substrate promiscuity of inositol 1,4,5-trisphosphate kinase driven by structurally-modified ligands and active site plasticity.

Marquez-Monino, M.A.Ortega-Garcia, R.Whitfield, H.Riley, A.M.Infantes, L.Garrett, S.W.Shipton, M.L.Brearley, C.A.Potter, B.V.L.Gonzalez, B.

(2024) Nat Commun 15: 1502-1502

  • DOI: https://doi.org/10.1038/s41467-024-45917-5
  • Primary Citation of Related Structures:  
    8PP8, 8PP9, 8PPA, 8PPB, 8PPC, 8PPD, 8PPE, 8PPF, 8PPG, 8PPH, 8PPI, 8PPJ

  • PubMed Abstract: 

    D-myo-inositol 1,4,5-trisphosphate (InsP 3 ) is a fundamental second messenger in cellular Ca 2+ mobilization. InsP 3 3-kinase, a highly specific enzyme binding InsP 3 in just one mode, phosphorylates InsP 3 specifically at its secondary 3-hydroxyl group to generate a tetrakisphosphate. Using a chemical biology approach with both synthetised and established ligands, combining synthesis, crystallography, computational docking, HPLC and fluorescence polarization binding assays using fluorescently-tagged InsP 3 , we have surveyed the limits of InsP 3 3-kinase ligand specificity and uncovered surprisingly unforeseen biosynthetic capacity. Structurally-modified ligands exploit active site plasticity generating a helix-tilt. These facilitated uncovering of unexpected substrates phosphorylated at a surrogate extended primary hydroxyl at the inositol pseudo 3-position, applicable even to carbohydrate-based substrates. Crystallization experiments designed to allow reactions to proceed in situ facilitated unequivocal characterization of the atypical tetrakisphosphate products. In summary, we define features of InsP 3 3-kinase plasticity and substrate tolerance that may be more widely exploitable.


  • Organizational Affiliation

    Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Blas Cabrera, CSIC, Serrano 119, 28006, Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inositol-trisphosphate 3-kinase A
A, B
279Homo sapiensMutation(s): 0 
Gene Names: ITPKA
EC: 2.7.1.127
UniProt & NIH Common Fund Data Resources
Find proteins for P23677 (Homo sapiens)
Explore P23677 
Go to UniProtKB:  P23677
PHAROS:  P23677
GTEx:  ENSG00000137825 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23677
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP (Subject of Investigation/LOI)
Query on ANP

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
06G (Subject of Investigation/LOI)
Query on 06G

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B]
D-myo-inositol 1,4,6-trisphosphate
C6 H15 O15 P3
MMWCIQZXVOZEGG-LKKUUOETSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
L [auth B]
M [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.653α = 90
b = 97.919β = 90
c = 192.066γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
REFMACphasing
Cootmodel building
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ANPClick on this verticalbar to view detailsBest fitted 06GClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2020-117400GB-100
Spanish Ministry of Economy and CompetitivenessSpainBFU2017-89913-P

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Database references