The three-dimensional architecture of the class I ligase ribozyme.
The class I ligase ribozyme catalyzes a Mg(++)-dependent RNA-ligation reaction that is chemically analogous to a single step of RNA polymerization. Indeed, this ribozyme constitutes the catalytic domain of an accurate and general RNA polymerase ribozyme. The ligation reaction is also very rapid in both single- and multiple-turnover contexts and thus is informative for the study of RNA catalysis as well as RNA self-replication. Here we report the initial characterization of the three-dimensional architecture of the ligase. When the ligase folds, several segments become protected from hydroxyl-radical cleavage, indicating that the RNA adopts a compact tertiary structure. Ribozyme folding was largely, though not completely, Mg(++) dependent, with a K(1/2[Mg]) < 1 mM, and was observed over a broad temperature range (20 degrees C -50 degrees C). The hydroxyl-radical mapping, together with comparative sequence analyses and analogy to a region within 23S ribosomal RNA, were used to generate a three-dimensional model of the ribozyme. The predictive value of the model was tested and supported by a photo-cross-linking experiment.
Bergman
Nicholas H
NH
Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA.
Lau
Nelson C
NC
Lehnert
Valerie
V
Westhof
Eric
E
Bartel
David P
DP
D000818:Animals; D003432:Cross-Linking Reagents; D006801:Humans; D017665:Hydroxyl Radical / Q000378:metabolism; D008027:Light; D008274:Magnesium / Q000378:metabolism; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000378:metabolism*; D013696:Temperature
D003432:Cross-Linking Reagents; D016337:RNA, Catalytic; D017665:Hydroxyl Radical; D008274:Magnesium