Structure of a self-splicing group II intron catalytic effector domain 5: parallels with spliceosomal U6 RNA.

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 structur

SUBMITTER: Seetharaman M 

PROVIDER: S-EPMC1370903 | biostudies-literature | 2006 Feb

REPOSITORIES: biostudies-literature