The Role of snRNAs in Spliceosomal Catalysis - Progress in Molecular Biology and Translational Science - page 202

this folding arrangement. 68 Taken together, current structural data suggest
that the three functionally critical regions in U6 are not only juxtaposed
in the activated spliceosomes, but also in protein-free U6/U2 complexes.
Thus, the spontaneous three-dimensional folding of the in vitro -assembled
U6/U2 complex is close to the functionally requisite structure that these
snRNAs assume in the spliceosome. 16
Butcher and colleagues 27,69 have determined the solution structure of a
fragment of the yeast U6-U2 complex that contains theU6 ISL and surround-
ing regions. Interestingly, they found that this truncated U6-U2 complex
forms a four-way junction that bears similarities to the proposed structure
for human U6-U2 complex and domain V of group II introns
( Fig. 6.5 ). 13,24,53 In their structure, the U6 ISL contains additional base pairs
at its base that incorporate the catalytic AGC triad into the ISL in a position
identical to the AGC triad in domain V. In addition, the longer U6 ISL shows
strong similarities in size and the overall structure to the solution structure of
domain V. 28 However, there are also important differences in the asymmetric
bulge region between the two structures. Formation of this elongated form of
ISL is mutually exclusive with the structure shown to exist in yeast based on
genetic studies 44,54,55 in which the AGC triad forms a short helix (helix Ib)
withU2 ( Fig. 6.5 ). It is possible, however, that helix Ib in the yeast spliceosome
is stabilized by proteins since the autonomous folding of RNA is likely to be
incompatible with the formation of such a short helix. Butcher and Brow 70
proposed a model in which formation of helix Ib is driven by proteins during
the structural rearrangements that occur between the two steps of splicing.
This model is very appealing because it also reconciles the difference between
the human and yeast U6-U2 structures deduced by genetic complementation
studies. Intriguingly, computer modeling of the structure of a U6/U2
construct that contains the ACAGAGA sequence suggests that the four-
way junction folding has the potential to bring the metal-binding region of
the U6 ISL (nucleotide U74 in human and U80 in yeast) within the vicinity
of the 5 0 splice site and the ACAGAGA domain. 69 Thus, similar to the case
with the hairpin ribozyme, a four-way junction in U6-U2 complex might
contribute to the formation of the active site of splicing reaction. 53,70
6. FUNCTIONALLY CRITICAL snRNA - METAL ION
INTERACTIONS
In addition to its potential role in stabilizing the proximity of the
ACAGAGA and the ISL in the folded structure of protein-free U6/U2