Eukaryotic protein carboxyl methyltransferase catalyzes a two-substrates reaction in which the methyl group of S-adenosylmethionine is transferred to the free carboxyl group of D-aspartyl and L-isoaspartyl-containing peptide or protein substrates. It has been previously shown that at least three binding sites are required for the interaction of adenosylmethionine with the enzyme and/or the protein substrate [Oliva A., Galletti P., Zappia V., Paik W. K. & Kim S. (1980) Eur. J. Biochem. 104, 595-6021, while very little is know concerning the structural requirements of the protein substrate.In this study several synthetic tripeptides were selected in order to elucidate the structural requirements of the methyl-accepting substrates. The results obtained with this series of peptides suggested that: (1) three residues appear to be the minimal length, so far identified, required for a productive enzyme-substrate interaction, several dipeptides being ineffective as substrates [McFadden P. N. & Clarke S. (1986) J . Biol. Chem. 261, 11 503 -11 51 11; (2) the isoaspartyl residue is not recognized unless its cc-amino group is involved in a carboamide bond; (3) an hydrogen atom on the amide linkage following the isoaspartyl residue is essential for both recognition and catalysis; (4) oligopeptides containing both D-aspartyl and D-isoaspartyl residues are not recognized by this methyltransferase. On the basis of these results, interaction sites between the peptide substrate and the enzyme molecule have been proposed. This paper also reports the first application of fast-atom-bombardment mass spectrometry to the detection of the products of the enzymatic methyl esterification reaction. By this soft ionization technique, the methylesterified peptides as well as the corresponding cyclic imides generated during the spontaneous demethylation process have been identified.Protein carboxyl methyl esterification, catalyzed by the enzyme S-adenosylmethionine : protein carboxy-0-methyl transferase (PCMT) has been recently proposed to be a crucial step in the repair or disposal of proteins containing altered aspartyl residues [l, 21. The above suggestion is supported by the experimental evidence that in eukaryotic proteins only L-isoaspartyl [3,6] residues are selectively recognized and modified by this enzyme.An enzyme playing such physiological roles should be endowed with a broad substrate specificity. A wide range of proteins can indeed be enzymatically methyl-esterified in vitro, although only to a substoichiometric extent [7], in that only a subpopulation of the protein substrate contains methylatable sites. Furthermore L-isoaspartyl-containing natural and synthetic peptides are stoichiometrically methylated in vitro by PCMT, regardless of the sequences surrounding the modification site [8 -111.Correspondence fo P. Galletti, Istituto di Biochimica delle Macromolecole, I Facolta di Medicina e Chirurgia, Via Costantinopoli 16, 1-80138 Napoli Abbreviations. PCMT, protein carboxyl-0-methyl transferase; AdoMet, S-adenosyl-L-methionine;...