The Group I Intron Ribozyme

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.  

As stated previously in the introductory section, T. R. Cech and co-workers reported on the first catalytic RNA or ribozyme, the self-splicing intron of the 

These interactions, plus others, stabilize the P4-P6 domain s conformation. Site-directed mutagenesis and chemical protection studies indicate that G212 in the P4 helix interacts with residues in the A-rich bulge, and the crystal structure shows interactions with A184 (02 G212-N1 A184 = 2.8 A, for example). The same sorts of interactions are found between the GAAA 

TABLE 6.1 Selected Distances for Group I Intron PDB IGID 

Nucleotide (PDB IGID Residue Number) Structural Element Ligand Atom (PDB IGID Symbol, Atom Number) Bond Distance (A) to Mg (6799), Mg (6800), Mg (6804), Mgf(6806), Mgi (6808), Mgf(6797)  

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Single-molecule FRET has been applied to the folding of the group I intron ribozyme (Lee et al, 2007a Russell et al, 2002 Zhuang et al, 2000), the group II intron ribozyme (Steiner et al., 2008), the VS ribozyme (Pereira et al, 2008), and the interaction of a tetraloop and its receptor (Hodak et al.,... 

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. 

Fig. 2. The P4-P6-domain of the group I intron of Tetrahymena thermophila. A Schematic representation of the secondary structure of the whole self-cleaving intron (modified after Cate et al. [34]). The labels for the paired regions P4 to P6 are indicated. The grey shaded region indicate the phylogenetically conserved catalytic core. The portion of the ribozyme that was crystallized is framed. B Three dimensional structure of the P4-P6 domain. Helices of the PSabc extension are packed against helices of the conserved core due to a bend of approximately 150° at one end of the molecule...

Another naturally occurring ribozyme which catalyzes phosphodiester transfer reactions is the hairpin ribozyme. The hairpin ribozyme has been the subject of a number of excellent review articles [24,25]. Several independent studies performed recently have indicated that the hairpin ribozyme has an interesting feature which distinguishes it from the aforementioned ribozymes mechanistically While the HHR, the group I intron, the HDV ribozyme and many other ribozymes that we are going to meet in this review are metalloenzymes and require divalent metal ions in their active sites for functional group activation, divalent metals ions only play a passive role (they are mainly required for cor-... 

It is clear that the analysis of thio effects, rescue experiments and other experiments with derivatives have contributed significantly to our understanding of the mechanism of the action of the large group I intron ribozyme of Tetmhymena. All the available data appear to support the Lewis acid catalysis for activation of the attacking nucleophile and enhancement of the leaving group that is shown in Fig. IIB. 

There are six ribozymes that have been successfully modified and/or adapted for use in therapeutic and functional genomic applications. These are the group I introns, RNAse P, the hammerhead and hairpin motifs, the hepatitis delta ribozyme and the reverse splicing reaction of group II introns. Each of these ribozymes requires a divalent metal cation for activity (usually Mg++), which may participate in the chemistry of the cleavage/ligation reaction and/or may be important for maintaining the structure of the ribozyme. 

Use of FPA to Study Helical Dynamics in a Complex RNA, with the Tetrahymena Group I Intron Ribozyme as an Example... 

Among the structurally more diverse RNA structures large polyads are also not unlikely, in particular when different polyad planes are linked by bases. Table 2 includes, for example, base hexad motifs in the P4-P6 group I intron ribozyme domain and the vitamin B12 aptamer. A heptad motif occurs in the ribosomal fiameshifting pseudoknot structure shown in Fig. 11. Finally, it should be noted that a base hexad has also been designed with metal-modified bases. In this case a central GG pairs is linked on both sides to AU pairs. This leads to the topology VI. 10(3224). 

Ribozymes Appeared. Tetrahymena thermophila revealed its group I intron ribozymes in Thomas Czeh s laboratory. Ribozymes catalyze their substrates ( like protein enzymes ) infra- and intermolecularly. The tetrahymena ribozyme s intramolecular catalysis consists of self-splicing (Golden BL et al Howard Hughes Medical Institute, Department of Chemistry and Biochemisby, University of Colorado, Boulder, CO. Science 1998 282 259-264). Alu ribonucleoproteins consists of polymerase Ill-transcribed Alu sequences and signal recognition proteins (SRP9/14) united. In the ribosome, these units inhibit IRES-mediated (internal ribosome enfry site) translation initiation (Ivanova E et al Nucleic Acids Res 2015 43 2874-2887). 

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