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Binding to E1 and E3 is mutually exclusive for the human autophagy E2 Atg3.

Yu Qiu1, Kay Hofmann, Julie E Coats

  • 1Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.

Protein Science : a Publication of the Protein Society
|November 5, 2013
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Summary

Autophagy ubiquitin-like protein (UBL) conjugation follows common enzyme cascade principles. The autophagy E2 enzyme, Atg3, competes for binding sites, enabling sequential loading and ligation for LC3 lipidation.

Keywords:
Atg12∼Atg5Atg3Atg7E1 enzymeE1‐E2 bindingE2 enzymeE2‐E3 bindingE3 enzymeautophagyubiquitin‐like protein

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Area of Science:

  • Cellular Biology
  • Biochemistry
  • Molecular Biology

Background:

  • Ubiquitin-like proteins (UBLs) are conjugated via E1-E2-E3 enzyme cascades.
  • Canonical UBL E2 enzymes bind E1 and E3 enzymes sequentially.
  • Autophagy UBL pathway enzymes are distinct, raising questions about conserved conjugation principles.

Purpose of the Study:

  • To investigate the organizational principles of the autophagy UBL, LC3, lipidation pathway.
  • To determine if autophagy UBL conjugation follows similar principles to canonical UBLs.

Main Methods:

  • Bioinformatic analysis to identify key regions in autophagy E2 enzyme, Atg3.
  • Experimental validation of Atg3 binding sites and functional inhibition of LC3 lipidation.
  • In vitro assays to assess competitive binding between E1 and E3 enzymes for Atg3.

Main Results:

  • A distinct region on autophagy E2, Atg3, was identified for binding to autophagy E3, Atg12∼Atg5-Atg16.
  • Peptides from this Atg3 region inhibited LC3 lipidation in vitro.
  • The E3-binding site on Atg3 overlaps with the E1 (Atg7) binding site, indicating competitive binding.

Conclusions:

  • The autophagy LC3 lipidation pathway shares organizational principles with canonical UBL conjugation.
  • Distinct structural features in autophagy enzymes mediate conserved functional mechanisms.
  • Atg3 likely cycles between Atg7 and the E3 complex for efficient LC3 lipidation.