Methylates cytosine to m5C at several positions in different tRNAs and pre-tRNAs containing intron. Able to modify tRNAs at all four positions (34, 40, 48 and 49) at which m5C has been found in tRNAs. May be involved in ribosome biogenesis as its disruption leads to increased sensitivity to the antibiotic paromomycin. cytidine(34) in tRNA precursor + S-adenosyl-L-methionine = 5-methylcytidine(34) in tRNA precursor + H(+) + S-adenosyl-L-homocysteine cytidine(40) in tRNA precursor + S-adenosyl-L-methionine = 5-methylcytidine(40) in tRNA precursor + H(+) + S-adenosyl-L-homocysteine cytidine(48) in tRNA + S-adenosyl-L-methionine = 5-methylcytidine(48) in tRNA + H(+) + S-adenosyl-L-homocysteine cytidine(49) in tRNA + S-adenosyl-L-methionine = 5-methylcytidine(49) in tRNA + H(+) + S-adenosyl-L-homocysteine Present with 16100 molecules/cell in log phase SD medium. Belongs to the class I-like SAM-binding methyltransferase superfamily. RsmB/NOP family. TRM4 subfamily.