Figure 1. Pathways of protein breakdown in mammalian cells. Most cytosolic and nuclear proteins in mammalian cells are broken down by the ubiquitin–proteasome pathway and some peptide products are utilized for MHC class I antigen presentation. The same pathway also mediates degradation of endoplasmic reticulum (ER) proteins (both integral membrane and luminal proteins) in the process called ER-associated degradation (ERAD). Some mitochondrial proteins are broken down by their own ATP-dependent proteases. Extracellular and autophagocytized proteins and most membrane proteins are broken down within the lysosome–endosomal compartment, which provides peptides for MHC class II antigen presentation. Exceptions (as indicated by dashed lines) are some membrane proteins that are broken down by the ubiquitin–proteasome pathway, and some cytosolic proteins that are degraded in lysosomes.

Figure 2. Ubiquitin–proteasome pathway. Protein substrate destined for degradation by the 26S proteasome is first conjugated to multiple molecules of Ubiquitin in a series of reactions involving ubiquitin-activating enzyme, E1, ubiquitin-carrier protein, E2, and ubiquitin-protein ligase, E3. Polyubiquitinated substrates are rapidly hydrolyzed by the 26S proteasome, and monomeric Ubiquitin is recycled by the action of deubiquitinating enzymes. The energy of ATP is required for Ubiquitin conjugation, unfolding of a substrate and its translocation into the inner cavities of the proteasome. Most peptides produced by proteasomes are further degraded to amino acids by endo- and exopeptidases in the cytosol and nucleus, but a small fraction of peptides escapes complete hydrolysis and are utilized for MHC class I antigen presentation.

Figure 3. Ubiquitin-conjugation cascade. The Ubiquitin is first activated by the ubiquitin-activating enzyme, E1, in an ATP-dependent reaction. In the second reaction, Ubiquitin is transferred to the ubiquitin-carrier protein, E2. The resultant high-energy E2~ubiquitin thioester intermediate mediates conjugation of activated Ubiquitin to the protein substrate in the presence of a ubiquitin-protein ligase, E3. New Ubiquitin moieties are linked to the previously bound Ubiquitin in successive rounds of conjugation.