Giardia intestinalis (flagellate)
Dicer, the specialized ribonuclease, triggers RNA interference (RNAi), a powerful gene-silencing process. The main catalytic function of Dicer is cleaving double-stranded RNA (dsRNA) into small fragments. These fragments are the hallmark of RNAi, called short interfering RNAs (siRNAs) or microRNAs (miRNAs). These small RNAs with RNAi machinery called RNA induced silencing complexes (RISC) bind to target mRNA, which has a complementary sequence. In other words, they act as the guide molecules which lead the RISC to target mRNA correctly. The typical length of the Dicer product is about 21 to 25 nucleotides long. Surprisingly, they have enough length to uniquely specify a single target gene in a eukaryotic genome. The intimate molecular mechanism which enables Dicer to generate ideal size small RNAs had not been known.
The structure shown here is that of the Dicer from Giardia intestinalis, causes giardiasis. This "hatchet-like" molecule is made up of an RNase III domain and a PAZ domain and another domain connecting them. Two RNase III domains form the blade and the PAZ domain makes up the base of the handle. The connecting long alpha-helix runs through the handle of the hatchet, encircled by the N-terminal domain called the platform domain. The platform domain is made up of an antiparallel beta sheet and three alpha helices. Each RNase III domain has a single catalytic metal ion, which hydrolyzes each strand of the dsRNA. The PAZ domain is an RNA binding module and also found in other siRNA- and miRNA-containing complexes. Measuring from the active site of the RNase III domain to the binding pocket of the 3' overhang of dsRNA in PAZ domain gives a distance of ~65 angstrom, which corresponds to approximately the 25 base pairs of dsRNA. The authors of the paper propose that Dicer works as a molecular ruler that measures and cleaves ~25 nucleotides from the end of a dsRNA.
Protein Data Bank (PDB)
author: Miho Higurashi