Mitochondrial S-adenosyl-L-methionine-dependent methyltransferase that catalyzes the formation of 5-methyl-uridine in tRNAs and 12S rRNA. Catalyzes the methylation of uridine at position 54 (m5U54) in all tRNAs. Specifically methylates the uridine in position 429 of 12S rRNA (m5U429). Does not affect RNA stability or mitochondrial translation. 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.