Group I introns

Figure 6.1 The group I intron exon-spUcing mechanism. (Adapted with permission from Figure 1 of reference 24. Copyright 2004, with permission from Elsevier.)...

The intron group I ribozymes feature common secondary structure and reaction pathways. Active sites capable of catalyzing consecutive phosphodi-ester reactions produce properly spliced and circular RNAs. Ribozymes fold into a globular conformation and have solvent-inaccessible cores as quantified by Fe(II)-EDTA-induced free-radical cleavage experiments. The Tetrahy-mem group I intron ribozyme catalyzes phosphoryl transfer between guanosine and a substrate RNA strand—the exon. This ribozyme also has been proposed to use metal ions to assist in proper folding, to activate the nucleophile, and to stabilize the transition state. ... 

Group I intron phosphotransesterification reactions are carried out by a conserved active site that contains a set of imperfect double helices named PI through P9. (See Figure 6.4.) P1-P9 helices are organized into three domains P1-P2, P4-P6, and P3-P9. Specifically, the Tetrahymena thermophila intron contains two sets of coaxially stacked helices that overlap to create the active site. These helices reside in two domains of approximately equal size P4-P6 and P3-P9. P domains are defined as base-paired regions, whereas J domains... 

Figure 6.4 Secondary structure of a group I intron ribozyme. (From Figure 1 of reference 13. Reprinted with permission of AAAS.) (See color plate)...

TABLE 6.1 Selected Distances for Group I Intron PDB IGID... 

Conserved in group I intron ribozymes. Invariant in group I intron ribozymes. 

The Cech group described an X-ray crystallographic structure of the group I intron from Tetrahymem thermophila in a Science magazine research article published in 1998 (PDB IGRZ). The 5.0-A resolution crystal structure included 247 nucleotides comprising most of the Tetrahymena thermophila intron. At this resolution, clear density for the ribozyme backbone was seen, and stacked bases were visualized as continuous tubes of electron density. 

Figure 6.7 A bacterial self-splicing group I intron with both exons (PDB 1U6B). Visualized using CambridgeSoft Chem3D Ultra 10.0 with notations in ChemDraw Ultra 10.0. (Printed with permission of CambridgeSoft Corporation.)...

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