tRNA pseudouridine synthase D (TruD) from Thermus thermophilus modifies U13 in tRNA^Asp, tRNA^Glu, and tRNA^Gln and U35 in tRNA^Tyr

A hypothetical mechanism illustrating how TruD distinguishes the recognition sequence in substrate RNAs from nonsubstrate RNAs. (A–C) The three distinct sites of the TruD recognition sequence found in T. thermophilus tRNAs are mapped onto the crystal structure of yeast tRNA^Phe (PDB id: 1EHZ). The TruD recognition sites are highlighted in red. (D) A close-up view of the Watson–Crick interaction between U13 and A22. The dashed lines show hydrogen bonding interaction. Note that the original C13–G22 base in yeast tRNA^Phe was replaced with U13–A22 using PyMOL. (E) A close-up view of the non-Watson–Crick interaction between U8 and A14. The dashed lines show hydrogen bonding interaction.