E2 conjugating enzyme required for the cytoplasm to vacuole transport (Cvt), and autophagy. Responsible for the E2-like covalent binding of phosphatidylethanolamine to the C-terminal Gly of atg8. The atg12-atg5 conjugate plays a role of an E3 and promotes the transfer of atg8 from atg3 to phosphatidylethanolamine (PE). This step is required for the membrane association of atg8. The formation of the atg8-phosphatidylethanolamine conjugates is essential for autophagy and for the cytoplasm to vacuole transport (Cvt) (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. atg12-conjugation plays a role in regulation of mitochondrial homeostasis and cell death, while it is not involved in PE-conjugation to atg8 and autophagy (By similarity). Belongs to the ATG3 family.