The ATG16L1 complex (consisting of ATG12, ATG5 and ATG16L1) functions as an E3-like ligase, mediating the transfer of LC3 ubiquitin-like proteins from the E2-like enzyme ATG3 to phosphatidylethanolamine (PE) in the expanding membrane (Tanida et al. 2002, Hanada et al. 2007, Fujita et al. 2008, Sakoh-Nakatogawa et al. 2013). In this final step of LC3 lipidation, the C-terminal glycine of the LC3 protein is conjugated to PE through an amide bond (Ichimura et al. 2000). This results in the lipidation of LC3 proteins at the curved membrane forming the autophagosome (Carlsson & Simonsen 2015). The resulting lipid-conjugated LC3 proteins are sometimes referred to as LC3-II. In yeast the LC3 family is represented by one protein, Atg8, which has a C-terminal ubiquitin-like domain that is preceded by a short N-terminal extension. The human LC3 family has six members (Slobodkin & Elazar 2013). The microtubule-associated protein-1 light chain proteins MAP1LC3A, MAP1LC3B and MAP1LC3C typically have their names shortened respectively to LC3A, LC3B and LC3C. The remaining family members are the gamma-aminobutyric acid (GABA)-receptor-associated proteins GABARAP, GABARAPL1 and GABARAPL2. The biological relevance of this expansion of Atg8 proteins in higher eukaryotes is largely unknown (Slobodkin & Elazar 2013, Wild et al. 2014).
ATG3 has a membrane-curvature-sensing domain that may allow it to detect lipid-packing defects at the rim of the growing phagophore (Nath et al. 2014). This function would localize the lipidation reaction of LC3 or GABARAP to the highly-curved surface at the edge of the growing phagophore (Carlsson & Simonsen 2015).
Lipidation of LC3 proteins enables them to associate with the autophagosomal membrane as it expands (Weidberg et al. 2010, 2011, Mizushima et al. 2011, Lamb et al. 2013). ATG proteins dissociate from the isolation membrane before it closes to create an autophagosome, while LC3 proteins remain attached on what becomes the inner autophagosome membrane surface (Klionsky 2005). LC3 proteins are thought to play a role in the expansion and closure of the isolation membrane (Geng & Klionsky 2008, Fujita et al. 2008, Weidberg et al. 2010, 2011).