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Updated: Sep 19, 2025

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CryoEM provides detailed insights into how VPS15 regulates VPS34 activity

Robyn Duttenhefner1, Subeksha Subedi1, Sangita C Sinha1

  • 1Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050, USA.

Trends in Biochemical Sciences
|June 19, 2025
PubMed

Insights

The VPS15 pseudokinase binds GTP and myristate, stabilizing inactive VPS34. Myristate release activates VPS34 for PI3P production on membranes.

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Cell Signaling

Background:

  • The class III phosphatidylinositol 3-kinase (PI3K) complex, including VPS34, is crucial for cellular processes.
  • Regulation of VPS34 activity is essential for maintaining cellular homeostasis.
  • VPS15 is a regulatory subunit that interacts with VPS34.

Purpose of the Study:

  • To elucidate the molecular mechanism by which VPS15 regulates VPS34 activity.
  • To understand the role of GTP binding and myristate sequestration in VPS15 function.
  • To investigate how VPS15 controls VPS34's kinase activity and membrane localization.

Main Methods:

  • Biochemical assays to study protein-ligand interactions.
  • Structural analysis of VPS15 and VPS34 complex.
  • In vitro kinase assays.
  • Cellular localization studies.

Main Results:

  • The VPS15 pseudokinase domain binds GTP and sequesters its N-terminal myristate.
  • This binding and sequestration stabilize inactive conformations of the VPS34 kinase domain.
  • Myristate release from VPS15 disrupts the inhibitory interaction and facilitates VPS34 membrane docking.
  • Activated VPS34 catalyzes phosphatidylinositol-3-phosphate (PI3P) production.

Conclusions:

  • VPS15 acts as a direct regulator of VPS34 kinase activity through GTP and myristate binding.
  • Myristate release is a key step in activating VPS34 for PI3P synthesis.
  • This mechanism highlights a novel regulatory pathway for PI3K signaling.
Keywords:
GTP-binding pseudokinaseN-myristate sequestrationautophagyclass III phosphatidylinositol 3-kinase (PI3KC3) or vacuolar protein sorting protein 34 (VPS34) complexescryo-electron microscopy (cryo-EM)vacuolar protein sorting protein 15 (VPS15)

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