FIGURE 1.

The conserved core structure of Group I introns. (A) Conserved secondary structure depicted using the conventional nomenclature (Burke et al. 1987). The additional intron-specific peripheral structural elements and their sites of insertion are indicated within the dotted boxes and are coded by cyan, orange, and lime colors representing Twort, Azoarcus, and Tetrahymena, respectively. The purple boxes indicate the positions where •OH footprints corresponding to the 10 topologically equivalent tertiary contacts are observed. (B,C) Superposition of the crystal structures of the three ribozymes (Twort-1Y0Q.pdb, Azoarcus-1ZZN.pdb, Tetrahymena-1X8W.pdb). The superimposed structures are either viewed from an angle such that the P4–P6–P5abc domains appear in the front (B) or from the opposite side, such that the P9.1–P9.2 and P7.1–P7.2 domains appear in the front. (C) The introns are color coded as in A. The backbones of the conserved core regions are shown as ribbons. The nucleotides within the 10 homologous tertiary contacts are shown as sticks. The peripheral domains of Twort (P7.1–7.2 and P9.1) and Tetrahymena (P5abc, P2–2.1, and P9.1–9.1a–9.2) are shown as semitransparent space-filled surfaces in cyan and lime, respectively. Since the peripheral structures are missing in the Tetrahymena crystal structure (1X8W), these domains were obtained from the phylogenetically derived 3D model (TtLSU.pdb) and the structure of the P4–P6 domain (1GID.pdb), and spatially oriented by superposing these structures on 1X8W.pdb. B and C were generated in PyMOL (DeLano 2009).