The Hammerhead Ribozyme: Structure, Catalysis, and Gene Regulation - Progress in Molecular Biology and Translational Science - page 15

Figure 1.3 Sequence arrangement and secondary structure model of rodent CLEC2d-
associated hammerhead ribozymes. Secondary structure of the mouse ribozyme
sequence is shown. The rat ribozyme single nucleotide- and base pair-differences are
indicated in boxes adjacent to the mouse sequence. The stop codon is denoted in white.
The “ substrate ” sequence is shown on a gray background. The insertion sequence sep-
arating the two ribozyme segments is abridged with a thick arrow, and helices are iden-
tified by roman numerals. Rat insertion length and distance to polyA site are in italics.
The predicted cleavage site is 3 0 of the active site cytosine (circled).
place of Loop I. Sequence alignment revealed remarkable conservation of
the hammerhead motif's catalytic core including nucleotides necessary to
establish the catalytically important tertiary interactions ( Fig. 1.5 ). Addi-
tional conservation is observable in the secondary structure in the form of
compensatory mutations that maintain the hammerhead's secondary struc-
ture ( Fig. 1.4 ). Structural similarity and specific association with orthologous
genes, including CLEC-like sequence in the platypus genome, 65 imply that
all 12 CLEC2 ribozymes share a common ancestor that arose before mono-
treme divergence from other therian lineages about 200 million years ago.
A large insertion between substrate and enzyme strands distinguishes the
CLEC2 ribozymes not only from other hammerhead ribozymes, but also
frommost known self-cleaving sequences. In rodent CLEC2 hammerheads,
the length of the sequence separating the two critical ribozyme domains