Disclosed is a novel method for improving an enzyme capable of deamidating a protein. A mutant enzyme can be designed by the following steps (1) and (2): (1) specifying at least one amino acid residue among amino acid residues corresponding to the amino acid residues located at position-35, position-38, position-39, position-40, position-41, position-42, position-43, position-45, position-46, position-49, position-79, position-80, position-81, position-82, position-83, position-84, position-103, position-104, position-105, position-106, position-117, position-142, position-143, position-146, position-166 and position-185 in the amino acid sequence depicted in SEQ ID NO:2 which is an amino acid sequence for a protein deamidase (an enzyme to be mutated); and (2) constructing an amino acid sequence having the substitution of the amino acid residue specified in step (1) by another amino acid residue or having the deletion of the amino acid residue specified in step (1) by using the amino acid sequence for the enzyme to be mutated as a base sequence.