PMID:16522645
| Citation |
Mokdad, A, Krasovska, MV, Sponer, J and Leontis, NB (2006) Structural and evolutionary classification of G/U wobble basepairs in the ribosome. Nucleic Acids Res. 34:1326-41 |
|---|---|
| Abstract |
We present a comprehensive structural, evolutionary and molecular dynamics (MD) study of the G/U wobble basepairs in the ribosome based on high-resolution crystal structures, including the recent Escherichia coli structure. These basepairs are classified according to their tertiary interactions, and sequence conservation at their positions is determined. G/U basepairs participating in tertiary interactions are more conserved than those lacking any interactions. Specific interactions occurring in the G/U shallow groove pocket--like packing interactions (P-interactions) and some phosphate backbone interactions (phosphate-in-pocket interactions)--lead to higher G/U conservation than others. Two salient cases of unique phylogenetic compensation are discovered. First, a P-interaction is conserved through a series of compensatory mutations involving all four participating nucleotides to preserve or restore the G/U in the optimal orientation. Second, a G/U basepair forming a P-interaction and another one forming a phosphate-in-pocket interaction are replaced by GNRA loops that maintain similar tertiary contacts. MD simulations were carried out on eight P-interactions. The specific GU/CG signature of this interaction observed in structure and sequence analysis was rationalized, and can now be used for improving sequence alignments. |
| Links |
PubMed PMC1390688 Online version:10.1093/nar/gkl025 |
| Keywords |
Base Pairing; Base Sequence; Conserved Sequence; Crystallography, X-Ray; Evolution, Molecular; Guanine/chemistry; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Phosphates/chemistry; RNA, Archaeal/chemistry; RNA, Bacterial/chemistry; RNA, Ribosomal/chemistry; RNA, Ribosomal, 16S/chemistry; RNA, Ribosomal, 23S/chemistry; RNA, Ribosomal, 5S/chemistry; Ribosomes/chemistry; Sequence Analysis, RNA; Uracil/chemistry |
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