H/ACA box RNP
Pyrococcus furiosus (archaea,thermophile)
Post-transcriptional modification is an essential process for making functional RNAs, including tRNA and rRNA, mature and able to fulfill their function. Pseudouridylation, an isomerization of uridine to pseudouridine, is a common post-transcriptional modification for functional RNAs. It uses either stand-alone enzymes that select the modification site via protein recognition or ribonucleoprotein (RNP) enzymes that specify target through complementary base pairs between an H/ACA guide RNA and a substrate RNA. The RNP is a member of the H/ACA box RNP family which is one of the major small nucleolar RNP (snoRNP) families. It uses an H/ACA box guide RNA for recognition of its substrate RNA via base pair complementarities, and its protein as a catalyst for the pseudouridylation reaction. It is reported that the substrate is mainly rRNA whose pseudouridylation is important for a ribosome assembly. RNPs mature rRNAs by modifying uridine on specific positions based on a variety of guide RNAs. That is, guide RNA’s complementarity allows position dependent modification.
The substrate-free structure of an entire archaeal H/ACA box RNP has been determined at 2.3Å resolution; it consists of 4 polypeptide subunits, Cbf5, Nop10, Gar1, L7ae, and of an H/ACA box guide RNA. The RNA-guided pseudouridylation starts with the binding of the guide RNA to the substrate RNA, followed by an enzymatic reaction catalyzed by Cbf5. The H/ACA box guide RNA has a linear single-hairpin structure with ACA and k-turn motifs at both ends, which bind proteins strongly. Due to the
complex contacts involved in the conserved motifs at both ends, a wide variety of internal loop region forming the pseudouridylation pocket are possible depending on the substrate RNAs. A substrate binding model suggests that the target uridine in the substrate RNA approaches to the active cleft on Cbf5. It also suggests that Gar1, which does not bind guide RNA directly, may control substrate loading and release. Contact patterns between each subunit were revealed from the crystal structure and a consensus structure of H/ACA RNPs, in which the RNA is used for recognition and the polypeptide for catalysis, was discovered. However, additional research is needed to determine the structure of H/ACA box RNP in higher organisms and to validate the substrate-attached model.
Protein Data Bank (PDB)
author: Naoya Fujita