Fig. 5.

Comparison of secondary structures, tertiary folds, and cleavage sites of HDV and hatchet ribozyme products. (A and B) Secondary structure schemes of HDV (A) and hatchet (B) ribozyme products (cleavage sites are highlighted by yellow stars and catalytic pockets by light pink shadows). Residues crucial for the cleavage reaction (C75 in HDV, and G31 in hatchet) are shown in red. Note that the color code highlights comparable stacks between HDV and hatchet RNA, and not consecutive stem numbering. (C and D) Cartoon representations of the tertiary structures of HDV (PDB code: 1DRZ) (C) and hatchet (D) ribozyme products. Labeling of cleavage sites, catalytic nucleosides in the pocket, and helix colors are as in A and B. (E) Catalytic pocket of HDV ribozyme product (PDB code: 1DRZ). The cleaved G1 terminus is shown in yellow, paired to U37, and stacked between G2-C36 and G38-C22 base pairs. The key residue C75 is unpaired but held in place by two base layers G28-C19 and G25-U20 from stem P3 and the junction base A65. (F) Catalytic pocket of hatchet ribozyme product. The cleaved U1 terminus is shown in yellow, paired to A19, and stacked between U2-A18 and G30-C20 base pairs. The key residue G31 is paired with C64 and stacked partially between G32-C62 and the ribose of A74′. Note that A74′ is also stacked with G30-C20 below the U1 terminus.