Structural Characterization of U-1915 in Domain IV from Escherichia Coli 23S Ribosomal RNA as 3-Methylpseudouridine

Mass spectrometry-based methods have been used to study post-transcriptional modification in the 1900–1974 nt segment of domain IV in 23S rRNA of Escherichia coli, a region which interacts with domain V in forming the three-dimensional structure of the peptidyl transferase center within the ribosome. A nucleoside constituent of Mr 258 (U*) which occurs at position 1915, within the highly modified oligonucleo-tide sequence 1911-ΨAACU*AΨ-1917, was characterized as 3-methylpseudouridine (m3Ψ). The assignment was confirmed by chemical synthesis of m3Ψ and comparison with the natural nucleoside by liquid chromatography-mass spectrometry. 3-Methylpseu-douridine is previously unknown in nature and is the only known derivative of the common modified nucleo-side pseudouridine thus far found in bacterial rRNA.