Mitochondrial S-adenosyl-L-methionine-dependent methyltransferase that catalyzes the formation of 5-methyl-uridine in tRNAs and 12S rRNA (PubMed:31948311, PubMed:34556860). Catalyzes the methylation of uridine at position 54 (m5U54) in all tRNAs (PubMed:31948311). Specifically methylates the uridine in position 429 of 12S rRNA (m5U429) (PubMed:31948311). Does not affect RNA stability or mitochondrial translation (PubMed:31948311). S-adenosyl-L-methionine + uridine(54) in tRNA = 5-methyluridine(54) in tRNA + H(+) + S-adenosyl-L-homocysteine a uridine in 12S rRNA + S-adenosyl-L-methionine = a 5-methyluridine in 12S rRNA + H(+) + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family.