Biogenesis of ribosomal subunits involves enzymatic modifications of rRNA that
fine-tune functionally important regions. The universally conserved prokaryotic
dimethyltransferase KsgA sequentially modifies two universally conserved
adenosine residues in helix 45 of the small ribosomal subunit rRNA, which is in
proximity of the decoding site. Here we present the cryo-EM structure of
Escherichia coli KsgA bound to an E. coli 30S at a resolution of 3.1 Å. The
high-resolution structure reveals how KsgA recognizes immature rRNA and binds
helix 45 in a conformation where one of the substrate nucleotides is flipped-out
into the active site. We suggest that successive processing of two adjacent
nucleotides involves base-flipping of the rRNA, which allows modification of the
second substrate nucleotide without dissociation of the enzyme. Since KsgA is
homologous to the essential eukaryotic methyltransferase Dim1 involved in 40S
maturation, these results have also implications for understanding eukaryotic
ribosome maturation.
