ArticleRNA (New York, N.Y.)2006
Structure of a self-splicing group II intron catalytic effector domain 5: parallels with spliceosomal U6 RNA.
Article in RNA (New York, N.Y.), 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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36 citing papers in PubMed, 70 citations in OpenAlex.
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- Structural features of a 3' splice site in influenza a.Biochemistry · 2015Article
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- Structural and functional insights into the N-terminus of Schizosaccharomyces pombe Cdc5.Biochemistry · 2014Article
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- Deriving quantitative dynamics information for proteins and RNAs using ROTDIF with a graphical user interface.Journal of biomolecular NMR · 2013Article
- Enhanced group II intron retrohoming in magnesium-deficient Escherichia coli via selection of mutations in the ribozyme core.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- The structural stabilization of the κ three-way junction by Mg(II) represents the first step in the folding of a group II intron.Nucleic acids research · 2013Article
- Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding RNA processing motif in Giardia lamblia.Nucleic acids research · 2012Article
- Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure.Journal of biomolecular NMR · 2012Article
- Multiple conformations of SAM-II riboswitch detected with SAXS and NMR spectroscopy.Nucleic acids research · 2012Article
- Biomass production of site selective 13C/15N nucleotides using wild type and a transketolase E. coli mutant for labeling RNA for high resolution NMR.Journal of biomolecular NMR · 2012Article
- Probing adenine rings and backbone linkages using base specific isotope-edited Raman spectroscopy: application to group II intron ribozyme domain V.Biochemistry · 2010Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Domain 5 (D5) is absolutely required for all catalytic functions of group II introns. Here we describe the solution NMR structure, electrostatic calculations, and detailed magnesium ion-binding surface of D5 RNA from the Pylaiella littoralis large ribosomal RNA intron (D5-PL). The overall structure consists of a hairpin capped by a GNRA tetraloop. The stem is divided into lower and upper helices of 8 and 5 bp, respectively, separated by an internal bulge. The D5-PL internal bulge nucleotides stack into the helical junction, resulting in a coupling between the bulge A25 and the closing base pair (G8-C27) of the lower helix. Comparison of the D5-PL structure to previously reported related structures indicates that our structure is most similar, in the helical regions, to the crystal structure of D5 from yeast Ai5gamma (D5-Ai5gamma) and the NMR structure of the U6 snRNA stem-loop region. Our structure differs in many respects from both the NMR and X-ray structures of D5-Ai5gamma in the bulge region. Electrostatic calculations and NMR chemical shift perturbation analyses reveal magnesium ion-binding sites in the tetraloop, internal bulge, and the AGC triad in the lower stem. Our results suggest that the structure, electrostatic environment, and the magnesium ion-binding sites within the tetraloop, bulge, and triad regions are conserved features of the splicing machinery of both the group II introns and the spliceosome that are likely key for catalytic function.
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