Structural Basis for Peptide Binding of α-N Terminal Methyltransferase from Saccharomyces cerevisiae

α-N terminal methylation is an ubiquitous post-translational modification that is conserved throughout prokaryotes and eukaryotes. ScNTM1 is an α-N terminal methyltransferase from Saccharomyces cerevisiae that methylate ribosomal proteins i.e., Rpl12ab and Rps25a/Rps25b. Here, the crystal structures of ternary complex of ScNTM1 with its cofactor S-adenosyl-L-homocysteine (SAH) and Rps25a-based hexapeptide [PPKQQL] at 1.0 Å and binary complex of ScNTM1 with SAH at the resolution of 1.1 Å are reported. The structure revealed that ScNTM1 adopts folding similar to the known structure of the members of NTM1 subfamily and the surface displayed the evolution-related variety. Comparative structure analysis of the ternary complex of ScNTM1with the human NRMT1 and NRMT2 demonstrated that most residues participating in substrate binding are conserved. The side chain of Tyr32 plays a key role to recognize the P2 and Q4 of the hexapeptide, which is further verified by point mutation and isothermal titration calorimetry (ITC) experiments in vitro. Structural alignment of the ternary and binary complexes indicates a slight shift occurring in some regions i.e., residues (25–36, 183–186, and 215–221) upon peptide binding. The work provides structural insights into the substrate recognition of ScNTM1.