GIR1 Catalyzes Three Different Reactions
GIR1 Branching Ribozyme | |
---|---|
Conserved secondary structure of GIR1 | |
Identifiers | |
Symbol | GIR1 |
Rfam | RF01807 |
Other data | |
RNA type | Intron |
Domain(s) | Naegleria |
In vitro, DiGIR1 catalyses three different reactions. The first one consists in hydrolysis of the scissil phosphate at the IPS site. This is the cleavage reaction observed with the full-length intron and several length variants with a relative low rate. The hydrolytic cleavage is irreversible and is considered as an in vitro artefact resulting from a miss-folding of the catalytic site to present the branch nucleotide (BP) correctly for the reaction. The second reaction,the natural one, is the branching reaction, in which a transesterification at the IPS site results in the cleavage of the RNA with a 3'OH and a downstream lariat cap made by joining of the first and the third nucleotide by a 2'-5' phosphodiester bond.
These products are the only products observed by analysis of cellular RNA. This branching reaction is in equilibrium with a third one: a ligation reaction. It is a very efficient reaction and it tends to mask the branching reaction during the in vitro branching experiments with the full-length intron and length variants that include more than 166 nucleotides upstream of the IPS.
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