Catalyzes the formation of 5-methyl-uridine at position 54 (m5U54) in tRNA. S-adenosyl-L-methionine + uridine(54) in tRNA = 5-methyluridine(54) in tRNA + H(+) + S-adenosyl-L-homocysteine Activated by magnesium ions. Contains a N-terminal TRAM-like domain, an iron-sulfur cluster in the central region and a C-terminal catalytic domain. The tRNA-binding site is probably formed at the interface of the three regions. Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family.