An isopeptidase is a protease enzyme that hydrolyzes isopeptide bonds, or amide bonds that occur outside the main chain in a polypeptide chain.
In eukaryotes, enzymes with isopeptidase activity are often involved in this pathway; all five classes of deubiquitinating enzymes have isopeptidase activity.
[3][4] Isopeptidases have also been identified in prokaryotes that express lasso peptides, or peptides with a knotted conformation established by the presence of a non-main-chain linkage between an acidic amino acid and the peptide's N-terminus to form the knot.
(Some lasso peptides also have topological complexity conferred by disulfide bonds.)
Isopeptidase enzymes linearize the peptides by cleaving the isopeptide bond.