Abstract of the PDB Structure's related Publication:
The eukaryotic small ribosomal subunit carries only four ribosomal (r) RNA methylated bases, all close to important functional sites. N(7)-methylguanosine (m(7)G) introduced at position 1575 on 18S rRNA by Bud23-Trm112 is at a ridge forming a steric block between P- and E-site tRNAs. Here we report atomic resolution structures of Bud23-Trm112 in the apo and S-adenosyl-L-methionine (SAM)-bound forms. Bud23 and Trm112 interact through formation of a β-zipper involving main-chain atoms, burying an important hydrophobic surface and stabilizing the complex. The structures revealed that the coactivator Trm112 undergoes an induced fit to accommodate its methyltransferase (MTase) partner. We report important structural similarity between the active sites of Bud23 and Coffea canephora xanthosine MTase, leading us to propose and validate experimentally a model for G1575 coordination. We identify Bud23 residues important for Bud23-Trm112 complex formation and recruitment to pre-ribosomes. We report that though Bud23-Trm112 binds precursor ribosomes at an early nucleolar stage, m(7)G methylation occurs at a late step of small subunit biogenesis, implying specifically delayed catalytic activation. Finally, we show that Bud23-Trm112 interacts directly with the box C/D snoRNA U3-associated DEAH RNA helicase Dhr1 supposedly involved in central pseudoknot formation; this suggests that Bud23-Trm112 might also contribute to controlling formation of this irreversible and dramatic structural reorganization essential to overall folding of small subunit rRNA. Our study contributes important new elements to our understanding of key molecular aspects of human ribosomopathy syndromes associated with WBSCR22 (human Bud23) malfunction.
Bud23 is involved in ribosome biogenesis. Deletion of Bud23 leads to severely impaired growth, reduced levels of small (40S) ribosomal subunit, and a block in processing 20S rRNA to 18 rRNA, a late step in 40S maturation (White et al. 2008 ). Evolutionary, Bud23 belongs to the S-adenosylmethionine-dependent-Rossman-fold methyltransferase superfamily and is related to small-molecule methyltransferase. Nonetheless, it has been demonstrated that Bud23 deficient mutants do not show a methylated SSU-18S G1575, indicating a clear role in this transcript methylation. Indeed, Bud23 methylates the N7 atom of the highly conserved G1575 (m7G) located in a single-stranded region between stem 29 and hairpin 42 of domain III in 18S rRNA (in E. coli it is the G1338, not methylated). Bud23 has a dual function, it is involved in the processes of rRNA modification and nuclear export of small subunit pre-particles. Synthetic lethality was demonstrated with Rps15p, an essential ribosomal protein involved in the nuclear export of small subunits pre-particles. Interaction with Trm112 is required for Bud23 activity.