N-alpha-acetyltransferase that acetylates the N-terminus of proteins that retain their initiating methionine (PubMed:19744929, PubMed:22311970, PubMed:21900231, PubMed:27484799). Has a broad substrate specificity: able to acetylate the initiator methionine of most peptides, except for those with a proline in second position (PubMed:27484799). Also displays N-epsilon-acetyltransferase activity by mediating acetylation of the side chain of specific lysines on proteins (PubMed:19744929). Autoacetylates in vivo (PubMed:19744929). The relevance of N-epsilon-acetyltransferase activity is however unclear: able to acetylate H4 in vitro, but this result has not been confirmed in vivo (PubMed:19744929). Component of N-alpha-acetyltransferase complexes containing NAA10 and NAA15, which has N-alpha-acetyltransferase activity (PubMed:16507339, PubMed:29754825, PubMed:27484799, PubMed:32042062). Does not influence the acetyltransferase activity of NAA10 (PubMed:16507339, PubMed:27484799). However, it negatively regulates the N-alpha-acetyltransferase activity of the N-terminal acetyltransferase A complex (also called the NatA complex) (PubMed:32042062). The multiprotein complexes probably constitute the major contributor for N-terminal acetylation at the ribosome exit tunnel, with NAA10 acetylating all amino termini that are devoid of methionine and NAA50 acetylating other peptides (PubMed:16507339, PubMed:27484799). Required for sister chromatid cohesion during mitosis by promoting binding of CDCA5/sororin to cohesin: may act by counteracting the function of NAA10 (PubMed:17502424, PubMed:27422821). acetyl-CoA + N-terminal L-methionyl-L-alanyl-[protein] = CoA + H(+) + N-terminal N(alpha)-acetyl-L-methionyl-L-alanyl-[protein] acetyl-CoA + N-terminal L-methionyl-L-seryl-[protein] = CoA + H(+) + N-terminal N(alpha)-acetyl-L-methionyl-L-seryl-[protein] acetyl-CoA + N-terminal L-methionyl-L-valyl-[protein] = CoA + H(+) + N-terminal N(alpha)-acetyl-L-methionyl-L-valyl-[protein] acetyl-CoA + N-terminal L-methionyl-L-threonyl-[protein] = CoA + H(+) + N-terminal N(alpha)-acetyl-L-methionyl-L-threonyl-[protein] acetyl-CoA + N-terminal L-methionyl-L-lysyl-[protein] = CoA + H(+) + N-terminal N(alpha)-acetyl-L-methionyl-L-lysyl-[protein] acetyl-CoA + N-terminal L-methionyl-L-leucyl-[protein] = CoA + H(+) + N-terminal N(alpha)-acetyl-L-methionyl-L-leucyl-[protein] acetyl-CoA + N-terminal L-methionyl-L-phenylalanyl-[protein] = CoA + H(+) + N-terminal N(alpha)-acetyl-L-methionyl-L-phenylalanyl-[protein] acetyl-CoA + N-terminal L-methionyl-L-tyrosyl-[protein] = CoA + H(+) + N-terminal N(alpha)-acetyl-L-methionyl-L-tyrosyl-[protein] kcat is 7.2 min(-1) with M-L-G-P-E peptide. kcat is 7.2 min(-1) with M-L-D-P-E peptide. kcat is 10.9 min(-1) with M-I-G-P-E peptide. kcat is 6.8 min(-1) with M-L-A-L-I peptide. kcat is 2.3 min(-1) with M-L-G-T-G peptide. kcat is 5.6 min(-1) with M-L-G-T-E peptide. Optimum pH is 7.5-8.0. Component of the N-terminal acetyltransferase E (NatE) complex at least composed of NAA10, NAA15 and NAA50 (PubMed:16507339, PubMed:29754825, PubMed:32042062). Interacts with NAA10 (PubMed:16507339, PubMed:32042062). Interacts with NAA15 (PubMed:16507339, PubMed:29754825, PubMed:32042062). Predominantly interacts with NAA15 in the N-terminal acetyltransferase A complex (NatA complex); the interactions reduce the acetylation activity of the NatA complex (PubMed:16507339, PubMed:32042062). Component of the N-terminal acetyltransferase E (NatE)/HYPK complex at least composed of NAA10, NAA15, NAA50 and HYPK (PubMed:32042062). Within the complex interacts with NAA15 (PubMed:32042062). Its capacity to interact with the NatA complex is reduced by HYPK (PubMed:32042062). Interacts with NAA35 (By similarity). Localizes to the cytoplasm in interphase cells (PubMed:17502424). Belongs to the acetyltransferase family. GNAT subfamily.