Involved in mitochondrial ribosome assembly. 5-methylcytosine rRNA methyltransferase that probably is involved in mitochondrial ribosome small subunit (SSU) maturation by methylation of mitochondrial 12S rRNA at position 911; the function is independent of MTERFD2/MTERF4 and assembled mitochondrial ribosome large subunit (LSU). Targeted to LSU by MTERFD2/MTERF4 and probably is involved in a final step in ribosome biogenesis to ensure that SSU and LSU are assembled. In vitro can methylate 16S rRNA of the LSU; the methylation is enhanced by MTERFD/MTERF4. a cytidine in rRNA + S-adenosyl-L-methionine = a 5-methylcytidine in rRNA + H(+) + S-adenosyl-L-homocysteine a cytidine in tRNA + S-adenosyl-L-methionine = a 5-methylcytidine in tRNA + H(+) + S-adenosyl-L-homocysteine Heterodimer with MTERFD2/MTERF4; this interaction seems to be required for NSUN4 recruitment to the mitochondrial large ribosomal subunit. Additional isoforms seem to exist. Embryonic lethal. Belongs to the class I-like SAM-binding methyltransferase superfamily. RsmB/NOP family.