Aspartic acid in protein isomerizes autocatalytically to isoaspartate via succinimide intermediate in vitro and in vivo. We have determined the crystal structures of Ustilago sphaerogena ribonuclease U2 with an isoaspartate residue and hen egg-white lysozymes with a succinimide intermediate and with an isoaspartate residue at 1.8 Å resolution. These crystal structures reveal that the isomerizations of aspartic acids induce structural changes on proteins, which result in modifying the function and physical properties of the proteins.