An NMR study of the helix V-loop E region of the 5S RNA from Escherichia coli

P. Zhang, P. B. Moore
1989 Biochemistry  
Experiments are described that complete the assignment of the imino proton N M R spectrum of the fragment 1 domain from the 5s R N A of Escherichia coli. Most of the new assignments fall in the helix V-loop E portion of the molecule (bases 70-78 and 98-106), the region most sensitive to the binding of ribosomal protein L25. The spectroscopic data are incompatible with the standard, phylogenetically derived model for 5s RNA, which makes all the base pairs possible in loop E with the sequences
more » ... th the sequences aligned in parallel ( C 7 M 1 0 6 , C 7 1 4 1 0 5 , etc.) [see Delihas et al. (1984) Prog. Nucleic Acid Res. Mol. Biol. 31, 161-1901. Furthermore, the alternative loop E model proposed for spinach chloroplast 5s R N A by Romby et al. [(1988) Biochemistry 27,4721-47301 does not apply to the closely homologous 5s R N A from E. coli. The 5 s RNAs from E. coli and spinach chloroplasts do not have the same secondary structures in solution despite their strong sequence homologies, and neither appears to conform to the standard model for 5 s R N A in the loop E region. F. igure 1 shows the sequence of the 5 s RNA from Escherichia coli drawn in the secondary structure derived for it by comparative sequence analysis. Like the larger rRNAs, it is a series of stem-loop structures, and its hydrogen-bonded stems tend to be short and to include non-Watson-Crick base pairs [see Delihas et al. (1984) l. We have been studying this molecule by nuclear magnetic resonance (NMR),' concen-* Abbreviations: NMR, nuclear magnetic resonance; NOE, nuclear Overhauser effect; poly(U), poly(uridy1ic acid).
doi:10.1021/bi00437a015 pmid:2669961 fatcat:c5s7qk2imfffdmagfuvs3hsjxa