Autophagy, a process that results in the lysosomal-dependent degradation of cytosolic compartments, is carried out by the autophagosome, which is a double-membrane vesicle whose formation is catalyzed by several autophagyrelated gene (Atg) proteins. Atg4D (autophagy-related gene 4D), also known as APG4D or AUTL4, is a 474 amino acid protein that localizes to the cytoplasm and belongs to the C-54 family of cysteine proteases. Expressed predominately in skeletal muscle, but also present in testis, Atg4D functions as a cysteine protease that is required for autophagy and functions to specifically cleave the C-terminal region of target proteins, thereby allowing the target proteins to bind to autophagosomes. The enzymatic activity of Atg4D is inhibited by N-ethylmaleimide, a thiol reactive compound that is capable of modifying cystine residues in proteins and peptides.