A method for improving the degree of deamidation (%) and the deamidation rate when deamidating a milk protein by an enzyme which exerts a deamidating effect by acting directly on an amide group of a protein without cleaving a peptide bond or crosslinking the protein is provided. A method for denaturing a milk protein enzymatically is also provided. A preliminarily denatured milk protein is deamidated by a protein deamidating enzyme which exerts a deamidating effect by acting directly on an amide group of a protein having a molecular weight of 5,000 or more without cleaving a peptide bond or crosslinking the protein. Such an enzyme can be used also for denaturing a milk protein.