E2 conjugating enzyme required for the cytoplasm to vacuole transport (Cvt), autophagy, and mitochondrial homeostasis. Responsible for the E2-like covalent binding of phosphatidylethanolamine to the C-terminal Gly of atg8-like proteins (gabarap, gabarapl1, gabarapl2 or map1lc3a). The atg12-atg5 conjugate plays a role of an E3 and promotes the transfer of atg8-like proteins from atg3 to phosphatidylethanolamine (PE). This step is required for the membrane association of atg8-like proteins. The formation of the atg8-phosphatidylethanolamine conjugates is essential for autophagy and for the cytoplasm to vacuole transport (Cvt). Also acts as an autocatalytic E2-like enzyme, catalyzing the conjugation of atg12 to itself, atg12 conjugation to atg3 playing a role in mitochondrial homeostasis but not in autophagy. atg7 (E1-like enzyme) facilitates this reaction by forming an E1-E2 complex with atg3 (By similarity). Interacts with atg7 and atg12. The complex composed of atg3 and atg7 plays a role in the conjugation of atg12 to atg5. Conjugated to atg12 at Lys-241. ATG12-conjugation plays a role in regulation of mitochondrial homeostasis and cell death, while it is not involved in PE-conjugation to ATG8-like proteins and autophagy (By similarity). Belongs to the ATG3 family.