Structural basis of the autophagy-related LC3/Atg13 LIR complex: recognition and interaction mechanism

Structure. 2014 Jan 7;22(1):47-58. doi: 10.1016/j.str.2013.09.023. Epub 2013 Nov 27.

Abstract

Autophagy is a bulk degradation pathway that removes cytosolic materials to maintain cellular homeostasis. The autophagy-related gene 13 (Atg13) and microtubule associate protein 1 light chain 3 (LC3) proteins are required for autophagosome formation. We demonstrate that each of the human LC3 isoforms (LC3A, LC3B, and LC3C) interacts with Atg13 via the LC3 interacting region (LIR) of Atg13. Using X-ray crystallography, we solved the macromolecular structures of LC3A and LC3C, along with the complex structures of the LC3 isoforms with the Atg13 LIR. Together, our structural and binding analyses reveal that the side-chain of Lys49 of LC3 acts as a gatekeeper to regulate binding of the LIR. We verified this observation by mutation of Lys49 in LC3A, which significantly reduces LC3A positive puncta formation in cultured cells. Our results suggest that specific affinity of the LC3 isoforms to the Atg13 LIR is required for proper autophagosome formation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptor Proteins, Signal Transducing / chemistry*
  • Adaptor Proteins, Signal Transducing / genetics
  • Adaptor Proteins, Signal Transducing / metabolism
  • Amino Acid Sequence
  • Animals
  • Autophagy / genetics*
  • Autophagy-Related Proteins
  • Binding Sites
  • Crystallography, X-Ray
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Fibroblasts / cytology
  • Fibroblasts / metabolism*
  • Gene Expression Regulation
  • HEK293 Cells
  • Humans
  • Lysine / genetics
  • Lysine / metabolism
  • Mice
  • Microtubule-Associated Proteins / chemistry*
  • Microtubule-Associated Proteins / genetics
  • Microtubule-Associated Proteins / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Mutation
  • Phagosomes / genetics*
  • Phagosomes / metabolism
  • Phagosomes / ultrastructure
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • Protein Isoforms / chemistry
  • Protein Isoforms / genetics
  • Protein Isoforms / metabolism
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism

Substances

  • ATG13 protein, human
  • Adaptor Proteins, Signal Transducing
  • Autophagy-Related Proteins
  • MAP1LC3B protein, human
  • Microtubule-Associated Proteins
  • Protein Isoforms
  • Recombinant Proteins
  • light chain 3, human
  • Lysine