8PPG | pdb_00008ppg

Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosyl 1,3,4,6-tetrakisphosphate/ADP/Mn after reaction

PDB DOI: https://doi.org/10.2210/pdb8PPG/pdb

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

Deposited: 2023-07-07 Released: 2024-02-28
Deposition Author(s): Marquez-Monino, M.A., Gonzalez, B.
Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities, Spanish Ministry of Economy and Competitiveness

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.243 (Depositor), 0.246 (DCC)
R-Value Work:
0.206 (Depositor), 0.214 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

PubMed: 38374076 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-024-45917-5
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 66.64 kDa
Atom Count: 4,694
Modeled Residue Count: 517
Deposited Residue Count: 558
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol-trisphosphate 3-kinase A	A, B	279	Homo sapiens	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23677
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
46I (Subject of Investigation/LOI) Query on 46I Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B]	G [auth A], N [auth B]	beta-D-glucopyranosyl 1,3,4,6-tetrakisphosphate C₆ H₁₆ O₁₈ P₄ HWPKOYDCMYQLFR-UKFBFLRUSA-N		Interactions Focus chain G [auth A] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain N [auth B]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B]	F [auth A], M [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain M [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain L [auth B]	C [auth A] D [auth A] E [auth A] J [auth A] K [auth B] C [auth A], D [auth A], E [auth A], J [auth A], K [auth B], L [auth B], P [auth B], Q [auth B], R [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain H [auth A]	H [auth A], I [auth A], O [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B]