Abstract of the PDB Structure's related Publication:
In Escherichia coli, RlmB catalyzes the methylation of guanosine 2251, a modification conserved in the peptidyltransferase domain of 23S rRNA. The crystal structure of this 2'O-methyltransferase has been determined at 2.5 A resolution. RlmB consists of an N-terminal domain connected by a flexible extended linker to a catalytic C-terminal domain and forms a dimer in solution. The C-terminal domain displays a divergent methyltransferase fold with a unique knotted region, and lacks the classic AdoMet binding site features. The N-terminal domain is similar to ribosomal proteins L7 and L30, suggesting a role in 23S rRNA recognition. The conserved residues in this novel family of 2'O-methyltransferases cluster in the knotted region, suggesting the location of the catalytic and AdoMet binding sites.
RlmB is a SPOUT-type of methyltransferase catalyzing formation of Gm at the conserved position 2251 in the peptidyltransferase domain V of large subunit rRNA (hairpin 80, also named P-loop). The ortholog SPOUT enzyme in S. cerevisiae is Mrm1 (formerly Pet56) catalyzing Gm at equivalent position 2270 (S. cerevisiae numbering) in large subunit mitochondrial rRNA. In cytoplasmic rRNA, the same conserved Gm is catalyzed at position 2619 (S. cerevisiae numbering) by C/D box RNP, guided by snR67. AdoMet is the donor of methyl group. The N-terminal domain of E. coli RlmB is similar to those in ribosomal proteins L7 and L30.