8PPD

Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with DL-6-deoxy-6-hydroxy-methyl-scyllo-inositol 1,2,4-trisphosphate/ATP/Mn

Summary for 8PPD

• Entry DOI: 10.2210/pdb8ppd/pdb
• Related: 8PP8 8PP9 8PPA 8PPB 8PPC
• Descriptor: Inositol-trisphosphate 3-kinase A, SULFATE ION, ADENOSINE-5'-TRIPHOSPHATE, ... (6 entities in total)
• Functional Keywords: inositol polyphosphate, insp, inositol kinase, ip3k, calcium, insp3, ip3, ipk, ip3 3-k, transferase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 66419.46

Authors

Marquez-Monino, M.A.,Gonzalez, B. (deposition date: 2023-07-07, release date: 2024-02-28, Last modification date: 2024-03-27)

Primary citation

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.
Substrate promiscuity of inositol 1,4,5-trisphosphate kinase driven by structurally-modified ligands and active site plasticity.
Nat Commun, 15:1502-1502, 2024

PubMed Abstract: D-myo-inositol 1,4,5-trisphosphate (InsP) is a fundamental second messenger in cellular Ca mobilization. InsP 3-kinase, a highly specific enzyme binding InsP in just one mode, phosphorylates InsP 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, we have surveyed the limits of InsP 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-kinase plasticity and substrate tolerance that may be more widely exploitable.

PubMed: 38374076
DOI: 10.1038/s41467-024-45917-5

Experimental method

X-RAY DIFFRACTION (1.77 Å)