8PP9

Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with scyllo-inositol 1,2,3,5-tetrakisphosphate/ADP/Mn


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4IM (Subject of Investigation/LOI)
Query on 4IM

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
scyllo-inositol 1,2,3,5-tetrakisphosphate
C6 H16 O18 P4
CIPFCGZLFXVXBG-FAEUDGQSSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
K [auth B]
L [auth B]
E [auth A],
F [auth A],
G [auth A],
K [auth B],
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],
N [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.504α = 90
b = 97.509β = 90
c = 191.487γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
REFMACphasing
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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