Activates the ATG1 kinase in a nutritional condition dependent manner through the TOR pathway, leading to autophagy (PubMed:26442587, PubMed:24793651). Involved in ATG9 and ATG23 cycling through the pre-autophagosomal structure (By similarity). Also involved in cytoplasm to vacuole transport (Cvt) and more specifically in Cvt vesicle formation (PubMed:24793651). Seems to play a role in the switching machinery regulating the conversion between the Cvt pathway and autophagy (By similarity). Finally, ATG13 is also required for glycogen storage during stationary phase (By similarity). Hypophosphorylated form interacts with ATG1 to form the ATG1-ATG13 kinase complex (PubMed:24793651). The ATG1-ATG13 complex interacts with the ATG17-ATG29-ATG31 complex through direct interaction with ATG17 (PubMed:24793651). Interacts with VAC8 (By similarity). The minimum ATG1-binding domain (residues 441 to 500) comprises two alpha-helices and a linker connecting them (PubMed:24793651). Hyperphosphorylated under nutrient-rich conditions (PubMed:24793651). Starvation and TOR inactivation results in ATG13 partial dephosphorylation leading to ATG1-binding (PubMed:24793651). Dephosphorylation induces ATG17-binding (PubMed:24793651). Impairs ATG17 localization to the preautophagosomal structure (PubMed:24793651). Still forms preautophagosomal structures (PAS) in proximity to the vacuolar membrane (PubMed:26442587). Kluyveromyces marxianus proteins are shorter in length and have a more ordered secondary structure than their S.cerevisiae counterparts, which might contribute to the superior thermotolerance and solubility (PubMed:26442587). K.marxianus could be therefore useful as a new model organism for further elucidation of the molecular details of autophagy (PubMed:26442587). Belongs to the ATG13 family. Fungi subfamily.