A mutant RNA pseudoknot that promotes ribosomal frameshifting in mouse mammary tumor virus.
A single A-->G mutation that changes a potential A.U base pair to a G.U pair at the junction of the stems and loops of a non-frameshifting pseudoknot dramatically increases its frameshifting efficiency in mouse mammary tumor virus. The structure of the non-frameshifting pseudoknot APK has been found to be very different from that of pseudoknots that cause efficient frameshifting [Kang,H., Hines,J.V. and Tinoco,I. (1995) J. Mol. Biol. , 259, 135-147]. The 3-dimensional structure of the mutant pseudoknot was determined by restrained molecular dynamics based on NMR-derived interproton distance and torsion angle constraints. One striking feature of the mutant pseudoknot compared with the parent pseudoknot is that a G.U base pair forms at the top of stem 2, thus leaving only 1 nt at the junction of the two stems. The conformation is very different from that of the previously determined non-frameshifting parent pseudoknot, which lacks the A.U base pair at the top of the stem and has 2 nt between the stems. However, the conformation is quite similar to that of efficient frameshifting pseudoknots whose structures were previously determined by NMR. A single adenylate residue intervenes between the two stems and interrupts their coaxial stacking. This unpaired nucleotide produces a bent structure. The structural similarity among the efficient frameshifting pseudoknots indicates that a specific conformation is required for ribosomal frameshifting, further implying a specific interaction of the pseudoknot with the ribosome.
Kang
H
H
Department of Chemistry, University of California, Berkeley CA 94720-1460, USA.
Tinoco
I
I
D000225:Adenine; D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D003198:Computer Simulation; D018965:Frameshifting, Ribosomal; D006147:Guanine; D009682:Magnetic Resonance Spectroscopy; D008324:Mammary Tumor Virus, Mouse / Q000235:genetics*; D051379:Mice; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D017354:Point Mutation; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics*; D013816:Thermodynamics; D014498:Uracil
D012367:RNA, Viral; D014498:Uracil; D006147:Guanine; D000225:Adenine