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The lonepair triloop: a new motif in RNA structure
Jung C Lee1, Jamie J Cannone, Robin R Gutell
1The University of Texas at Austin, College of Pharmacy, 1 University Station, A1900, Austin, TX 78712-0120, USA.
Journal of Molecular Biology
|December 11, 2002
Summary
The lonepair triloop (LPTL) is a newly identified RNA motif crucial for 3D structure and function. Found in rRNAs and tRNAs, LPTLs often interact with proteins and are vital for ribosomal activity.
Area of Science:
- Structural Biology
- RNA Biology
- Biochemistry
Background:
- The lonepair triloop (LPTL) is an RNA structural motif characterized by a single base-pair followed by a three-nucleotide hairpin loop.
- This motif is found in various RNA molecules, including ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs).
Purpose of the Study:
- To identify and characterize the lonepair triloop (LPTL) motif in RNA structures.
- To evaluate the prevalence, structural features, and functional implications of LPTLs in rRNAs and tRNAs.
Main Methods:
- Covariation analysis was initially used to identify potential LPTL motifs in 16S and 23S rRNAs.
- Crystal structures of ribosomal subunits (Thermus thermophilus 30S and Haloarcula marismortui 50S) were analyzed to confirm LPTL authenticity and discover new instances.
- Detailed structural analysis of identified LPTLs in rRNA and tRNA crystal structures.
Main Results:
- 24 LPTL examples were identified in 5S, 16S, and 23S rRNAs, as well as tRNA structures.
- LPTLs are typically located adjacent to regular helices, stabilized by coaxial stacking.
- The majority of LPTLs (22/24) participate in tertiary interactions, contributing to the overall 3D architecture and function.
- Non-standard base-pairing is common within LPTLs, with U:A being the most frequent lonepair.
- LPTLs are often found in conserved regions of rRNAs, including those involved in ribosomal function like peptidyl transferase activity.
- Approximately half of the LPTLs are associated with ribosomal proteins.
Conclusions:
- The lonepair triloop (LPTL) is a significant RNA structural motif with diverse base-pairing and conformational subtypes.
- LPTLs play crucial roles in RNA tertiary structure, stability, and function, particularly within the ribosome.
- The prevalence and conserved nature of LPTLs suggest their importance in fundamental biological processes across all domains of life.