2f88
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Solution NMR structure of domain 5 from the Pyaiella littoralis (PL) group II intron
OverviewOverview
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.
About this StructureAbout this Structure
2F88 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
Structure of a self-splicing group II intron catalytic effector domain 5: parallels with spliceosomal U6 RNA., Seetharaman M, Eldho NV, Padgett RA, Dayie KT, RNA. 2006 Feb;12(2):235-47. PMID:16428604
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