ArticleStructure (London, England : 1993)2019
Dynamics of Substrate Processing by PPIP5K2, a Versatile Catalytic Machine.
Article in Structure (London, England : 1993), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 14 citations in OpenAlex.
- Structural insights into the development of inhibitors for inositol phosphate kinases.FEBS letters · 2026Review
- Inositol pyrophosphate kinases in health and disease.FEBS letters · 2026Review
- Shared genetic architecture between Parkinson's disease and self-reported sleep-related traits implicates theSleep advances : a journal of the Sleep Research Society · 2026Article
- A small signaling domain controls PPIP5K phosphatase activity in phosphate homeostasis.Nature communications · 2025Article
- From Data to Knowledge: Systematic Review of Tools for Automatic Analysis of Molecular Dynamics Output.Frontiers in pharmacology · 2022Review
- ITPK1 is an InsPMolecular plant · 2021Article
- Metabolism and Functions of Inositol Pyrophosphates: Insights Gained from the Application of Synthetic Analogues.Molecules (Basel, Switzerland) · 2020Review
- A two-way switch for inositol pyrophosphate signaling: Evolutionary history and biological significance of a unique, bifunctional kinase/phosphatase.Advances in biological regulation · 2020Review
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
Processing of substrates by enzymes can only be fully understood through their conformational dynamics; this is particularly true for the diphosphoinositol pentakisphosphate kinase PPIP5K2, an enzyme with critical roles in cell signaling and bioenergetic homeostasis. PPIP5K2 is remarkable for the reversible nature of its kinase activity, its unique ligand-stimulated ATPase activity, and the substrate traveling between two ligand-binding sites. Here we use molecular dynamics and data analysis techniques to rationalize these PPIP5K2 activities, thereby increasing our understanding of complex enzymatic mechanisms. In particular, we demonstrate how the enzyme's distinctive, ratchet-like mechanism harnesses the energy of random fluctuations to significantly reduce the entropy toll for intramolecular substrate transfer. We show that pre-reaction pulling forces along the reaction coordinate are predictive of the various PPIP5K2 catalytic activities. An unexpected possibility, raised by these computational studies, that 3,5-IP8 might be a substrate for dephosphorylation was experimentally interrogated and confirmed in a luciferase assay.
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