Structural pathway for PI3-kinase regulation by VPS15 in autophagy

By Annan (Zeke) Cook, BSc, Minghao Chen, PhD, Thanh Nguyen, PhD, Ainara Claveras Cabezudo, MSc, Grace Khuu, BSc, Shanlin Rao, PhD, Samantha N. Garcia, Mingxuan Yang, Anthony T. Iavarone, Xuefeng Ren, PhD, Michael Lazarou, PhD, Gerhard Hummer, PhD, James Hurley

Published April 10, 2025

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Description

The class III phosphatidylinositol-3 kinase complexes I and II (PI3KC3-C1 and -C2) have vital roles in macroautophagy and endosomal maturation, respectively. We elucidated a structural pathway of enzyme activation through cryo-EM analysis of PI3KC3-C1. The inactive conformation of the VPS15 pseudokinase stabilizes the inactive conformation, sequestering its *N*-myristate in the N-lobe of the pseudokinase. Upon activation, the myristate is liberated such that the VPS34 lipid kinase catalyzes PI3P production on membranes. The VPS15 pseudokinase domain binds tightly to guanosine triphosphate (GTP), and stabilizes a web of interactions to autoinhibit the cytosolic complex and to promote the activation upon membrane binding. These findings show in atomistic detail how the VPS34 lipid kinase is activated in the context of a complete PI3K complex.

Identifier (DOI)

10.1126/science.adl3787

Tags

Cell biology
Molecular Dynamics simulation (MD)
Original Research
PI3KC3-C1 complex
Rab GTPases
Recombinant
Structural biology

Team

Team Hurley

Program

Collaborative Research Network

Theme

PD Functional Genomics

Meet the Authors

Annan (Zeke) Cook, BSc

Key Personnel: Team Hurley,

University of California, Berkeley
Minghao Chen, PhD

Key Personnel: Team Hurley,

University of California, Berkeley
Thanh Nguyen, PhD

Key Personnel: Team Hurley,

Walter and Eliza Hall Institute of Medical Research
Ainara Claveras Cabezudo, MSc

Key Personnel: Team Hurley,

Max Planck Institute of Biophysics
Grace Khuu, BSc

Key Personnel: Team Hurley,

Monash University
Shanlin Rao, PhD

Key Personnel: Team Hurley,

Max Planck Institute of Biophysics
Samantha N. Garcia

External Collaborator
Mingxuan Yang

External Collaborator
Anthony T. Iavarone

External Collaborator
Xuefeng Ren, PhD

Key Personnel: Team Hurley,

University of California, Berkeley
Michael Lazarou, PhD

Co-PI (Core Leadership): Team Hurley,

Monash University
Gerhard Hummer, PhD

Collaborating PI: Team Hurley,

Max Planck Institute of Biophysics
James Hurley

Lead PI (Core Leadership): Team Hurley,

University of California, Berkeley