Autophagin-2 (ATG4A, MEROPS identifier C54.002) is a cysteine endopeptidase required for autophagy, an intracellular degradation system found only in eukaryotes [, ]. Once induced, double membrane-bound vesicles called autophagosomes engulf cytoplasm, even whole organelles and invading bacteria, and deliver them to the lysosome for degradation. Autophagins cleave proteins required for autophagosome development, such as gamma-aminobutyric acid receptor-associated protein (GABARAP), gamma-aminobutyric acid receptor-associated protein-like 2 (GATE-16), and microtubule-associated protein light chain 3 (LC3). GABARAP and GATE-16 seem to be better substrates than LC3B for ATG4A [, , ].