Abstract of the PDB Structure's related Publication:
N(2)-Methylguanine 966 is located in the loop of Escherichia coli 16 S rRNA helix 31, forming a part of the P-site tRNA-binding pocket. We found yhhF to be a gene encoding for m(2)G966 specific 16 S rRNA methyltransferase. Disruption of the yhhF gene by kanamycin resistance marker leads to a loss of modification at G966. The modification could be rescued by expression of recombinant protein from the plasmid carrying the yhhF gene. Moreover, purified m(2)G966 methyltransferase, in the presence of S-adenosylomethionine (AdoMet), is able to methylate 30 S ribosomal subunits that were purified from yhhF knock-out strain in vitro. The methylation is specific for G966 base of the 16 S rRNA. The m(2)G966 methyltransferase was crystallized, and its structure has been determined and refined to 2.05A(.) The structure closely resembles RsmC rRNA methyltransferase, specific for m(2)G1207 of the 16 S rRNA. Structural comparisons and analysis of the enzyme active site suggest modes for binding AdoMet and rRNA to m(2)G966 methyltransferase. Based on the experimental data and current nomenclature the protein expressed from the yhhF gene was renamed to RsmD. A model for interaction of RsmD with ribosome has been proposed.
This methyltransferase catalyzes the formation of m2G966 in the loop of hairpin 31 of 16S rRNA within a pre-30S ribosome. A purified complex containing stoichiometric amounts of proteins S7, S9, and S19 bound to 16S rRNA possess the same RsmD methylation properties as 30S subunits. Structure of E.coli RsmD methyltransferase was determined and compared with the one of the M. jannaschii RsmC ortholog, specific for m2G1207 of the same 16S rRNA. RsmD and RsmC both posses a common MTase domain in the C-terminus (Rossmann-fold) and a variable region in the N-terminus that is related to the YbiN family of MTases (formation of m6A1618 by RlmF). Sequence/structure comparison suggests that both rRNA:m2G MTases are very closely related to RNA and DNA:m6A MTases and that these two enzyme families share common architecture of the active site and presumably a similar mechanism of methyl group transfer onto the exocyclic amino group of their target bases. Notice, adjacent to G966, a m5C967 has been found. The corresponding E. coli RsmB enzyme catalyzing m5C967 synthesis works in vitro only on free 16S rRNA; the presence of ribosomal proteins S7, S9 and S19 inhibit formation of m5C967 in vitro.
RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited--bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure.