NMR analysis of helix I from the 5S RNA of Escherichia coli

Abstract

The structure of helix I of the 5S rRNA from Escherichia coli has been determined using a nucleolytic digest fragment of the intact molecule. The fragment analyzed, which corresponds to bases (-1)-11 and 108-120 of intact 5S rRNA, contains a G-U pair and has unpaired bases at its termini. Its proton resonances were assigned by two-dimensional NMR methods, and both NOE distance and coupling constant information have been used to calculate structural models for it using the full relaxation matrix algorithm of the molecular dynamics program XPLOR. Helix I has A-type helical geometry, as expected. Its most striking departure from regular helical geometry occurs at its G-U, which stacks on the base pair to the 5' side of its G but not on the base pair to its 3' side. This stacking pattern maximizes interstrand guanine-guanine interactions and explains why the G-U in question fails to give imino proton NOE's to the base pair to 5' side of its G. These results are consistent with the crystal structures that have been obtained for wobble base pairs in tRNAPhe [Mizuno, H., & Sundaralingam, M. (1978) Nucleic Acids Res. 5, 4451-4461] and A-form DNA [Rabbinovich, D., Haran, T., Eisenstein, M., & Shakked, Z. (1988) J. Mol. Biol. 200, 151-161]. The conformations of the terminal residues of helix I, which corresponds to bases (-1)-11 and 108-120 of native 5S RNA, are less well-determined, and their sugar puckers are intermediate between C2' and C3'-endo, on average.

Two distinct structural elements of 5S rRNA are needed for its import into human mitochondria

“…(A) Human 5S rRNA secondary structure (mfold, corrected manually according to structural studies published). Sites of protein binding are colored (Baudin et al 1991;Chow et al 1992;White et al 1992;Allison et al 1993;Wimberly et al 1993;Szymanski et al 2000;Huber et al 2001;Lu et al 2003;Zuker 2003). (B) The overall mutation map of the human 5S rRNA obtained in this work.…”

RNA tertiary structure of the HIV RRE domain II containing non-Watson-Crick base pairs GG and GA: molecular modeling studies

“…At present, only a few X-ray crystal structures of tRNA molecules (12,13) and RNA double helices (14), as well as nuclear magnetic resonance (NMR) spectra data (15)(16)(17)(18) for small stem-loop and hairpin structures have been *To whom correspondence should be addressed determined at high resolution. Recently, the structures of DNA duplex (19) incorporating non-Watson-Crick base pair G:A and RNA double helix including G:U and C:U have been reported (14).…”

“…In the model M3, 15 Effects of water molecules and Na+ in the G:G base pair. The structure of the G:G base pair in the model M3 shows an unusual structural feature (Figure 6b).…”

Initial analysis of 750 MHz NMR spectra of selectively 15N‐G,U labelled E. coli 5S rRNA

“…For example, a previous study of the A-domain duplex (nucleotides l-11 and 108-119, Fig. 1) has identified the 'H chemical shifts of the imino hydrogens of the G-9-U-l 11 base pair [36]. A very strong GU imino-imino NOE characteristic of a GU base pair is observed at very similar 'H chemical shifts in the full 5S rRNA molecule (Fig.…”