Cbf5-Nop10-Gar1 complex (part of the pseudouridylation enzyme)
Pyrococcus furiosus (thermophile, archaea)
Box H/ACA riboncleoprotein complexes (H/ACA RNPs) post-transcriptionally isomerizes specific uridine residue in ribosomal RNA (rRNA) and small nucleolar RNA (snoRNA), and isomerized uridine is called pseudouridine. Pseudouridine is the most common modified nucleosides found in a diverse range of functional RNAs and it increases thermal stability of RNA helices that would otherwise be too flexible. H/ACA RNPs is composed of four proteins (Cbf5p, Nop10p, Nhp2p and Gar1p) and an guide RNA (gRNA). Among them, Cbf5 has strong sequence similarity to pseudouridine synthase TruB and is predicted to be the catalytic subunit of the H/ACA RNP. But unlike other pseudouridine synthetase, three accessory proteins and an guide RNA are necessary for pseudouridylation of target RNA. Past studies suggest that Nop10, Gar1 and NHP2 helps catalysis of cbf5 by modulating interaction between target RNA and guide RNA or putting the target RNA in the catalytic site of cbf5, but structural information had been lacking.
The structure shown here is the complex of three H/ACA proteins, Cbf5, Nop10 and Gar1 from Pyrococcus furiosus. Cbf5 consists of the catalytic domain and the PseudoUridine synthase and Archaeosine transglycosylase (PUA) domain and a long N-terminal tail. Cbf5 has a similar structure to TruB, and comparable distribution of functional residues in catalytic region indicates that a mechanism of interaction with the target uridine is conserved between Cbf5 and TruB. Nop10 is positioned near the target uridine pocket of Cbf5. Two conserved residues (Tyr14 and His31) of Nop10 form hydrogen bond with Arg204 and Glu202 of Cbf5 that is predicted to fix target uridine. Which indicates indirect stabilization of target RNA by Nop10. Gar1 seems to have no interaction between a target RNA and a guide RNA. Alternatively, Gar1 may stabilize a potential RNA binding element of Cbf5. Biochemical experiments conducted by authors indicate that Gar1 also protects Cbf5 from proteolysis.
Figure 1: The structure of Cbf5-Gal1-Nop10 complex. The three domains of Cbf5, catalytic domain, PUA domain, and N tail domain, are specified with pale green, cyan, and orange, respectively. The residues forming hydrogen bonds between Cbf5 and Nop10 (Glu202 and Arg204 in Cbf5, and Tyr14 and His31 in Nop10) are displayed in ball-and-stick expression.
Protein Data Bank (PDB)
author: Miho Higurashi