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. Author manuscript; available in PMC: 2012 Jun 1.
Published in final edited form as: Curr Opin Struct Biol. 2011 Apr 7;21(3):319–326. doi: 10.1016/j.sbi.2011.03.003

Figure 3. Proposed active sites based on RNase P, group I, and group II intron structures.

Figure 3

Whereas these catalytic RNAs require at least two metal ions, putatively magnesium (pink spheres), not all ribozymes contain metal cofactors within their active sites. In these large RNA molecules the overall active site structure does not change upon substrate binding and is largely preassembled, although correct substrate positioning likely enhances the rigidity of the active site and binding of catalytic metal ions. A) Structure of the T. maritima RNase P holoenzyme in complex with tRNA [11] (PDB 3OKB) shows components that comprise the active site scaffold. B) The Azoarcus group I intron (ribo-ΩG) with bound exons [42] (PDB 1ZZN). The group I active site (light blue) contains two A-rich regions and structurally conserved base triples that help to position an external nucleotide (ΩG, orange) and exons (red) during cleavage and ligation. The nucleophile and scissile bond for the ligation step are shown in yellow. C) Structure of the O. iheyensis group II intron shows three metal ions in the region where exon ligation occurs [33,46] (PDB 3EOG). Yellow dashed lines indicate metal-ligand interactions that are ≤ 3.0 Å for the RNase P and group II structures, and within ≤ 2.2 Å for the Azoarcus group I structure.