Hitherto enzymes that act on amino-acid residues in proteins have been named in different ways. For some of them, there has been no indication that the substrate is not a free amino acid, e.g. lysine,2-oxoglutarate dioxygenase (EC 1.14.11.4); for some 'peptidyl-' has been inserted before the name of the amino acid, e.g. peptidyl-lysine oxidase (EC 1.4.3.13), rather suggesting a C-terminal residue; for some the reverse practice, e.g. glutaminyl-peptide g-glutamyltransferase (EC 2.3.1.13), suggests an N-terminal residue; a fourth practice is seen in the name protein (arginine) methyltransferase (EC 2.1.1.23). Sometimes biochemsits have changed the name of the amino acid by replacing 'ine' with 'yl', but this indicates an acyl group rather than an amino-acid residue (thus an internal lysine residue is an acylated lysyl group), so this is not done in Enzyme Nomenclature. We plan to standardize by adding 'protein-', or the name of a particular protein, to the name of the residue that is the substrate. This has been done in Supplement 4, e.g.
EC 1.4.3.13, protein-lysine 6-oxidase
EC 1.14.11.4, procollagen-lysine,2-oxoglutarate 5-dioxygenase
EC 2.1.1.23, protein-arginine methyltransferase
EC 2.1.1.24, protein-glutamic(aspartic) methyltransferase
EC 2.1.1.43, histone-lysine methyltransferase
EC 2.1.1.60, calmodulin-lysine methyltransferase
EC 2.3.2.13, protein-glutamine glutaminase
1. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN), and Nomenclature Commission of IUB (NC-IUB), Newsletter 1983, Arch. Biochem. Biophys., 1983, 220, 321-324; Biochem. Internat., 1983, 6, following p 128; Biochem. J., 1983, 209, I-IV; Canad. J. Biochem. Cell Biol., 1983, 61, v-ix; Eur. J. Biochem., 1983, 131, 1-3; Hoppe-Seyler's Z. Physiol. Chem., 1983, 364, I-IV; Trends Biochem. Sci., 1983, 8, various issues.
Note The reference to Enzyme Nomenclature and Supplement 4 refers to the 1978 edition not the 1992 edition. Since 1992 EC 1.14.11.4 has been called procollagen-lysine 5-dioxygenase.