S-adenosyl-L-methionine-dependent methyltransferase that specifically methylates the N(3) position of a uridine in 25S rRNA. S-adenosyl-L-methionine + uridine in 25S rRNA = H(+) + N(3)-methyluridine in 25S rRNA + S-adenosyl-L-homocysteine Belongs to the class I-like SAM-binding methyltransferase superfamily. BMT5 family.