Catalyzes pseudouridylation at position 35 in U2 snRNA stem-loop II region which induces particular conformation of the mRNA-U2 snRNA duplex and places the nucleophile in an accessible position for the first step of splicing. Also catalyzes pseudouridylation at position 56 in U2 snRNA. Catalyzes also pseudouridylation at position 50 in 5S rRNA, position 13 in cytoplasmic tRNAs, and position 35 in pre-tRNA(Tyr). Pseudouridine residues in tRNAs may stabilize the local RNA conformation, favor interactions with protein partners and play an important role in the stabilization of the codon-anticodon interaction with mRNA. Also catalyzes pseudouridylation of mRNAs in response to heat shock: mediates pseudouridylation of mRNAs with the consensus sequence 5'-UGUAR-3'. uridine in 5S rRNA = pseudouridine in 5S rRNA uridine in snRNA = pseudouridine in snRNA uridine(13) in tRNA = pseudouridine(13) in tRNA a uridine in mRNA = a pseudouridine in mRNA Belongs to the pseudouridine synthase TruD family.