Structure of Deletion Mutant D5 RNA of a Group II Intron Ribozyme

Abstract

Nadukkudy V. Eldho and T. Kwaku Dayie Department of Chemistry and Biochemistry, University of Maryland, CollegePark, MD 20742. Group II introns are a class of self-catalytic ribozymes as well as mobile genetic elements found within the genes of all three kingdoms of life. They catalyze their own excision from pre-mRNA. It is hypothesized that pre-mRNA splicing may have evolved from group II introns due to the similar catalytic mechanism as well the structural similarity of the domain V substructure to the U6/U2 extended snRNA of spliceosome. The secondary structure of group II introns is characterized by six typical stem-loop structures, also called D1 to D6. The domain V (D5) is a highly conserved Mg2+ binding platform and through extensive interactions with other intron domains, arranges the catalytic core for self-splicing. D5 is arranged into two helices separated by a bulge in between, with the upper helix capped by GAAA tetraloop. The NMR titration of magnesium ions with D5 indicates that it act as a potential metal binding platform. Here we are reporting the structure of a deletion mutant of D5 which is defective in catalysis of the substrate, but effective in binding to D123 domain.