The MEROPS database of peptidases and proteolysis

A peptidase is an enzyme that catalyses the hydrolysis of a peptide bond that forms between amino acids in proteins and peptides. Peptidases are important for numerous post-translational modifications such as removal of the initiating methionine of cytoplasmic proteins, release of signal peptides and other transit peptides that target proteins for secretion or to organelles, activation of proteins by removal of propeptides (e.g. enzymes) and processing of polyproteins (e.g. peptide hormone precursors). Peptidases are also involved in protein catabolism, either to acquire or recycle components during feeding, protein turnover and degradation of misfolded proteins, or to switch off biological signals, as in apoptosis and receptor shedding. Peptidases are important components of pathogens (e.g. parasite invasion and feeding, viral polyprotein processing, processing of bacterial toxins) and are involved in pathology (e.g. cancer, rheumatoid arthritis, Alzheimer ’ s disease). The control of proteolysis is important because unchecked degradation can lead to pathological conditions, and the MEROPS database (Rawlings et al., 2008) includes not only peptidases but also their inhibitors (Rawlings et al., 2004). The latest release of the database is 8.4 (April 2009). Peptidases Assigning a biochemically uncharacterized sequence to a MEROPS identifier requires an alignment (built by MAFFT) and a phylogenetic tree derived from it (built by the UPGMA algorithm implemented in QuickTree). T