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 M(r) 258 (U*) which occurs at position 1915, within the highly modified oligonucleotide sequence 1911-Psi AACU*A Psi-1917, was characterized as 3-methylpseudouridine (m(3) Psi). The assignment was confirmed by chemical synthesis of m(3) Psi and comparison with the natural nucleoside by liquid chromatography-mass spectrometry. 3-Methylpseudouridine is previously unknown in nature and is the only known derivative of the common modified nucleoside pseudouridine thus far found in bacterial rRNA.