Multi-site-mediated entwining of the linear WIR-motif around WIPI β-propellers for autophagy

Jinqi Ren, Ruobing Liang, Wenjuan Wang, Dachuan Zhang, Li Yu and Wei Feng ()
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Jinqi Ren: Chinese Academy of Sciences
Ruobing Liang: Chinese Academy of Sciences
Wenjuan Wang: Chinese Academy of Sciences
Dachuan Zhang: Tsinghua University
Li Yu: Tsinghua University
Wei Feng: Chinese Academy of Sciences

Nature Communications, 2020, vol. 11, issue 1, 1-9

Abstract: Abstract WIPI proteins (WIPI1-4) are mammalian PROPPIN family phosphoinositide effectors essential for autophagosome biogenesis. In addition to phosphoinositides, WIPI proteins can recognize a linear WIPI-interacting-region (WIR)-motif, but the underlying mechanism is poorly understood. Here, we determine the structure of WIPI3 in complex with the WIR-peptide from ATG2A. Unexpectedly, the WIR-peptide entwines around the WIPI3 seven-bladed β-propeller and binds to three sites in blades 1–3. The N-terminal part of the WIR-peptide forms a short strand that augments the periphery of blade 2, the middle segment anchors into an inter-blade hydrophobic pocket between blades 2–3, and the C-terminal aromatic tail wedges into another tailored pocket between blades 1–2. Mutations in three peptide-binding sites disrupt the interactions between WIPI3/4 and ATG2A and impair the ATG2A-mediated autophagic process. Thus, WIPI proteins recognize the WIR-motif by multi-sites in multi-blades and this multi-site-mediated peptide-recognition mechanism could be applicable to other PROPPIN proteins.

Date: 2020
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DOI: 10.1038/s41467-020-16523-y

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