Sequence and structural conservation in RNA ribose zippers

Journal Article · Fri Mar 01 04:00:00 EST 2002 · Journal of Molecular Biology

DOI:https://doi.org/10.1016/S0022-2836(02)00515-6· OSTI ID:822616

Tamura, Makio ^[1]; Holbrook, Stephen R

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1. LBNL Library

The ribose zipper, an important element of RNA tertiary structure, is characterized by consecutive hydrogen-bonding interactions between ribose 20-hydroxyls from different regions of an RNA chain or between RNA chains. These tertiary contacts have previously been observed to also involve base backbone and base base interactions (A-minor type). We searched for ribose zipper tertiary interactions in the crystal structures of the large ribosomal subunit RNAs of Haloarcula marismortui and Deinococcus radiodurans, and the small ribosomal subunit RNA of Thermus thermophilus and identified a total of 97 ribose zippers. Of these, 20 were found in T. thermophilus 16 S rRNA, 44 in H. marismortui 23 S rRNA (plus 2 bridging 5 S and 23 S rRNAs) and 30 in D. radiodurans 23 S rRNA (plus 1 bridging 5 S and 23 S rRNAs). These were analyzed in terms of sequence conservation, structural conservation and stability, location in secondary structure, and phylogenetic conservation. Eleven types of ribose zippers were defined based on ribose base interactions. Of these 11, seven were observed in the ribosomal RNAs. The most common of these is the canonical ribose zipper, originally observed in the P4 P6 group I intron fragment. All ribose zippers were formed by antiparallel chain interactions and only a single example extended beyond two residues, forming an overlapping ribose zipper of three consecutive residues near the small subunit A-site. Almost all ribose zippers link stem (Watson Crick duplex) or stem-like (base-paired), with loop (external, internal, or junction) chain segments. About two-thirds of the observed ribose zippers interact with ribosomal proteins. Most of these ribosomal proteins bridge the ribose zipper chain segments with basic amino acid residues hydrogen bonding to the RNA backbone. Proteins involved in crucial ribosome function and in early stages of ribosomal assembly also stabilize ribose zipper interactions. All ribose zippers show strong sequence conservation both within these three ribosomal RNA structures and in a large database of aligned prokaryotic sequences. The physical basis of the sequence conservation is stacked base triples formed between consecutive base-pairs on the stem or stem-like segment with bases (often adenines) from the loop-side segment. These triples have previously been characterized as Type I and Type II A-minor motifs and are stabilized by base base and base ribose hydrogen bonds. The sequence and structure conservation of ribose zippers can be directly used in tertiary structure prediction and may have applications in molecular modeling and design.

• Research Organization: Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (US)
• Sponsoring Organization: National Institutes of Health (US)
• DOE Contract Number: AC03-76SF00098
• OSTI ID: 822616
• Report Number(s): LBNL--49731
• Journal Information: Journal of Molecular Biology, Journal Name: Journal of Molecular Biology Journal Issue: 3 Vol. 320; ISSN JMOBAK; ISSN 0022-2836
• Country of Publication: United States
• Language: English

Related Subjects

08 HYDROGEN
36 MATERIALS SCIENCE
59 BASIC BIOLOGICAL SCIENCES
99 GENERAL AND MISCELLANEOUS
ADENINES
AMINO ACIDS
BONDING
CRYSTAL STRUCTURE
FORECASTING
HYDROGEN
INTRONS
PROTEINS
RESIDUES
RIBOSE
RIBOSOMAL RNA
RIBOSOMAL RNA RNA RIBOSE ZIPPER RNA TERTIARY INTERACTION PROTEIN RNA INTERACTION A-MINOR MOTIF
RIBOSOMES
RNA
SIMULATION
STABILITY