This invention relates to a method of hydrolysis of the peptide bond between R1 and B in a specific designed amino acid sequence R1BXJZR3R2, where R1 represents a polypeptide of interest, R2 represents a sequence capable of specific binding to another component or molecule or another domain which needs to be cleaved, R3 represents an optional short peptide sequence, B represents a residue capable of accepting an acyl group, J represents a residue capable of metal ion binding, and X and Z represent amino acid residues, wherein the said method is based on a novel molecular mechanism of peptide bond hydrolysis, occurring in a specific complex of this metal ion with the BXJZ sequence. This method can be used to remove BXJZR3R2 domains in recombinant polypeptides, such as sequences capable of specific binding to another component or molecule to yield pure, unmodified R1 polypeptides of interest. The intermediate hydrolysis product can be reacted with other compounds to obtain derivatives of polypeptides of interest modified covalently at the C-terminus.