Fig. 4.

The LC3-interacting region (LIR) motif as a mechanistic basis for mitophagy. a LC3B structure (PDB 1UGM) [179], analyzed using Chimera [180]. Upper panel ribbon structure diagram indicating α-helices and β-sheets. LC3 proteins contain two N-terminal α-helices and a ubiquitin-like core formed from β strands. Hydrophobic pockets between β2 and α2 form the W-site, and between β2 and α3 form the L-site. Middle panel surface representation indicates topology of W- and L-sites (adapted from [49]), phosphorylated residues at S12 and T50, and putative binding sites for cardiolipin (R10 and R11) and ceramide (I35 and F52). Lower panel, N-terminal sequence alignments of LC3 homologues. Tcoffee alignment [181] of human LC3 member N-terminal regions using Jalview [182]. Blue shading indicates percentage identity, positively charged R, K and H residues, aligning to LC3B R10 and R11, are indicated in red. b The LIR motif, also known as Atg8 family-interacting motif (AIM), is a short linear peptide motif found in autophagy receptors, which binds LC3-II and thereby underlies selective autophagy. The LIR has a [W/Y/F]xx[L/I/V] core motif, and receptor-ligand interaction occurs through formation of an intermolecular β-sheet via hydrophobic interactions between the LIR motif and the conserved W and L sites on Atg8 proteins. c Sequence alignment of reported mitophagy receptor core LIR motifs and neighboring upstream and downstream regions. Phosphorylation can positively or negatively regulate LIR activity. d Two main groups of autophagy receptors target mitochondria. E3 ligase-mediated ubiquitylation of OMM proteins recruits ubiquitin-binding, LIR motif-containing receptors, which leads to the binding of receptors and engagement of sequestration by autophagosomes. Alternatively, a group of autophagy receptors contain a transmembrane domain and are constitutively targeted to the OMM. LIR activity of these mitophagy receptors is regulated by phosphorylation events