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PDBsum entry 1elh
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References listed in PDB file
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Key reference
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Title
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Nmr analysis of helix i from the 5s RNA of escherichia coli.
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Authors
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S.A.White,
M.Nilges,
A.Huang,
A.T.Brünger,
P.B.Moore.
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Ref.
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Biochemistry, 1992,
31,
1610-1621.
[DOI no: ]
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PubMed id
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Abstract
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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.
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Headers
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