1ELH

NMR ANALYSIS OF HELIX I FROM THE 5S RNA OF ESCHERICHIA COLI

Summary for 1ELH

• Entry DOI: 10.2210/pdb1elh/pdb
• Descriptor: RNA (5'-R(*UP*UP*GP*CP*CP*UP*GP*GP*CP*GP*GP*C)-3'), RNA (5'-R(*AP*AP*CP*UP*GP*CP*CP*AP*GP*GP*CP*AP*U)-3') (2 entities in total)
• Functional Keywords: rna, 5s ribosomal rna
• Biological source: Escherichia coli; More
• Total number of polymer chains: 2
• Total formula weight: 7960.84

Authors

White, S.,Moore, P. (deposition date: 1993-06-23, release date: 1994-01-31, Last modification date: 2024-05-22)

Primary citation

White, S.A.,Nilges, M.,Huang, A.,Brunger, A.T.,Moore, P.B.
NMR analysis of helix I from the 5S RNA of Escherichia coli.
Biochemistry, 31:1610-1621, 1992

PubMed 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.

PubMed: 1371071
DOI: 10.1021/bi00121a005

Experimental method

SOLUTION NMR