5DGI image
Deposition Date 2015-08-27
Release Date 2016-08-10
Last Version Date 2023-09-27
Entry Detail
PDB ID:
5DGI
Keywords:
Title:
Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP and 3,5-(PCP)2-IP4
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.85 Å
R-Value Free:
0.20
R-Value Work:
0.15
R-Value Observed:
0.15
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2
Gene (Uniprot):PPIP5K2
Chain IDs:A
Chain Length:330
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Cellular Cations Control Conformational Switching of Inositol Pyrophosphate Analogues.
Chemistry 22 12406 12414 (2016)
PMID: 27460418 DOI: 10.1002/chem.201601754

Abstact

The inositol pyrophosphate messengers (PP-InsPs) are emerging as an important class of cellular regulators. These molecules have been linked to numerous biological processes, including insulin secretion and cancer cell migration, but how they trigger such a wide range of cellular responses has remained unanswered in many cases. Here, we show that the PP-InsPs exhibit complex speciation behaviour and propose that a unique conformational switching mechanism could contribute to their multifunctional effects. We synthesised non-hydrolysable bisphosphonate analogues and crystallised the analogues in complex with mammalian PPIP5K2 kinase. Subsequently, the bisphosphonate analogues were used to investigate the protonation sequence, metal-coordination properties, and conformation in solution. Remarkably, the presence of potassium and magnesium ions enabled the analogues to adopt two different conformations near physiological pH. Understanding how the intrinsic chemical properties of the PP-InsPs can contribute to their complex signalling outputs will be essential to elucidate their regulatory functions.

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