tRNA cytosine C(5)-methyltransferase that methylates cytosine to 5-methylcytosine (m5C) in tRNAs at position 34 and 48 (PubMed:30646830). Trm4a and trm4b methylate different sets of tRNAs (PubMed:30646830). Also methylates cytosine to m5C at positions (60, 61 and 62) in tRNA(Asp) (PubMed:23074192). cytidine(48) in tRNA precursor + S-adenosyl-L-methionine = 5-methylcytidine(48) in tRNA precursor + H(+) + S-adenosyl-L-homocysteine cytidine(34) in tRNA precursor + S-adenosyl-L-methionine = 5-methylcytidine(34) in tRNA precursor + H(+) + S-adenosyl-L-homocysteine cytidine(60) in tRNA(Asp) + S-adenosyl-L-methionine = 5-methylcytidine(60) in tRNA(Asp) + H(+) + S-adenosyl-L-homocysteine cytidine(61) in tRNA(Asp) + S-adenosyl-L-methionine = 5-methylcytidine(61) in tRNA(Asp) + H(+) + S-adenosyl-L-homocysteine cytidine(62) in tRNA(Asp) + S-adenosyl-L-methionine = 5-methylcytidine(62) in tRNA(Asp) + H(+) + S-adenosyl-L-homocysteine Cells lacking both trm4a and trm4b show a mild resistance to calcium chloride. Belongs to the class I-like SAM-binding methyltransferase superfamily. RsmB/NOP family. TRM4 subfamily.