Catalyzes AdoMet-dependent formation of m5C in tRNA. Cytidine residue at either position 40 or position 48 is likely to be methylated. cytidine(48) in tRNA precursor + S-adenosyl-L-methionine = 5-methylcytidine(48) 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 Belongs to the class I-like SAM-binding methyltransferase superfamily. RsmB/NOP family.