E2 conjugating enzyme required for the cytoplasm to vacuole transport (Cvt) and autophagy. Required for selective autophagic degradation of the nucleus (nucleophagy) as well as for mitophagy which contributes to regulate mitochondrial quantity and quality by eliminating the mitochondria to a basal level to fulfill cellular energy requirements and preventing excess ROS production. 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 conjugate is essential for autophagy and for the cytoplasm to vacuole transport (Cvt). The atg8-PE conjugate mediates tethering between adjacent membranes and stimulates membrane hemifusion, leading to expansion of the autophagosomal membrane during autophagy (By similarity). Monomer. Interacts with atg8 through an intermediate thioester bond through the C-terminal Gly of atg8. Also interacts with the 40 amino acid C-terminal region of the E1-like atg7 enzyme. Interacts also with the atg12-atg5 conjugate. The N-terminal region is involved in phosphatidylethanolamine-binding and is required for atg8-PE conjugation. The flexible region (FR) is required for atg7-binding. The handle region (HR) contains the atg8 interaction motif (AIM) and mediates binding to atg8. It is crucial for the cytoplasm-to-vacuole targeting pathway (By similarity). Belongs to the ATG3 family.