Figure 1. Domain organization and secondary and three-dimensional structures of ribozymes.

Secondary structures are depicted in thick lines and are connected by thin black lines with arrows. Watson–Crick and non-canonical base pairs are shown as solid lines and circles, respectively. Bulged-out nucleotides are represented as triangles. Ribozymes with known three-dimensional structures are coloured according to secondary structure elements and domains. Three-dimensional structures, if available, are shown in a ribbon-and-stick representation below the secondary structures. The two nucleotides that lie adjacent to the scissile phosphate are indicated by red boxes. Nucleotides that are implicated in catalysis (panels a–f and i) or that are essential for molecular recognition (panel j) are indicated by yellow boxes. Black dashed squares and lines highlight important tertiary interactions. Coloured dashed lines indicate elements that are missing in the structure or that are substituted by non-natural sequences. a | Hammerhead ribozyme⁷⁶. b | Hairpin ribozyme⁷⁸. c | Hepatitis δ virus ribozyme⁷⁴. d | Varkud satellite (VS) ribozyme¹². e | CPEB3 ribozyme¹³. f | Human CoTC ribozyme¹⁴. g | Bacillus antracis glmS ribozyme; glucosamine-6-phosphate (GlcN6P) is represented as a red oval, with its interactions with RNA indicated by dashed lines⁶⁹. h | Bacillus subtilis RNase P, B-type⁷³. i | Domain organization of the group II intron, with IBS and EBS designating intron and exon binding sequences, respectively^21,22. The yellow-coloured A designates a conserved unpaired adenosine that participates in splicing. j | Asoarcus spp. BH72 group I intron in the state that precedes the second step of splicing⁷⁹. The internal guide sequence (IGS) aligns the 5′ and 3′ exons (ex), which are shown in grey. ωG and αG designate the 3′-terminal guanosine nucleotide of the intron and the external guanosine that is linked to the intron after the first step of splicing, respectively. Secondary structures in panels a, c, d, e, f, g, h and j are modified with permission from REF. 76 © (2006) Cell Press, REF. 117 © (2007) Cell Press, REF. 118 © (1995) National Academy of Sciences (USA), REF. 13 © (2006) American Association for the Advancement of Science, Nature REF. 14 © (2004) Macmillan Publishers Ltd, REF. 75 © (2006) American Association for the Advancement of Science and REF. 69 © (2007) Current Biology Ltd, REF. 119 © (2006) Elsevier Sciences and REF. 120 © (2005) Elsevier Sciences, respectively.