Initiates the repair of damaged proteins by catalyzing methyl esterification of L-isoaspartyl and D-aspartyl residues produced by spontaneous isomerization and racemization of L-aspartyl and L-asparaginyl residues in aging peptides and proteins (PubMed:12023972, PubMed:16923807, PubMed:20424163). Acts on EIF4EBP2, microtubule-associated protein 2, calreticulin, clathrin light chains a and b, Ubiquitin C-terminal hydrolase isozyme L1, phosphatidylethanolamine-binding protein 1, stathmin, beta-synuclein and alpha-synuclein (PubMed:16923807, PubMed:20424163). [protein]-L-isoaspartate + S-adenosyl-L-methionine = [protein]-L-isoaspartate alpha-methyl ester + S-adenosyl-L-homocysteine Monomer. The survival of Pcmt1 homozygous knockout mice drops significantly between the ages of 20 and 50 days compared to their wild-type counterparts (PubMed:12023972). They have 20 times more damaged aspartyl residues in their brains (PubMed:12023972). Belongs to the methyltransferase superfamily. L-isoaspartyl/D-aspartyl protein methyltransferase family.