The Role of snRNAs in Spliceosomal Catalysis - Progress in Molecular Biology and Translational Science - page 197

Figure 6.4 RNA-metal ion interactions in the snRNAs and pre-mRNA of spliceosomes
and domain V of group II introns (left and right, respectively). The central domains of
human U6 and 5 0 domain of human U2 snRNAs are shown. The pre-mRNA is shown
as a thick line, with the sequence of the branch site indicated. The ACAGAGA and
AGC sequences in U6 and domain V are boxed. Known metal ion-binding sites in the
pre-mRNA, U6, and domain V are indicated (Mg). Solid circles mark the sites of pho-
sphorothioate interference.
ACAGAGA box in U6 ( Fig. 6.2 ). Through a complex series of tertiary
interactions, a bulged nucleotide in the asymmetric internal loop of domain
V and two residues in J2/3 form base triples with the portion of the duplex at
the base of domain V that contains the AGC triad ( Fig. 6.2 , dashed lines).
This unusual arrangement, which brings together all the suspected active site
elements in group II introns, also participates in formation of inner sphere
binding sites for two metal ions which are likely to be involved in catalysis in
this system. 13 Interestingly, U6 contains the equivalent of all these sequences
that likely form the active site in group II introns. If the spliceosomal active
site indeed resembles that of group II introns, then U6 constitutes a major
part if not the entire spliceosomal active site. 12,14
In addition to the mechanistic and structural similarities discussed above,
recent studies have uncovered a number of additional parallels between the
two systems. For example, similar to the recently proven dispensability of
U2 snRNA in the spliceosome, the counterpart domain VI in group II
introns is also not essential for catalytic activity. However, in its absence,
the first step of splicing is performed through hydrolytic cleavage of
the 5 0 splice site rather than branching. 24,36 In another parallel between
the spliceosome and group II introns, it has recently been shown that the
spliceosomal active site can also catalyze hydrolytic cleavage reactions. In
spliceosomes stalled after the second step of splicing, the addition of manga-
nese ions to the reaction buffer results in release of cleaved 5 0 and 3 0 exons,