Abstract
The methylation of U1498 located in the 16S ribosomal RNA of Escherichia coli is an important modification affecting ribosomal activity. RsmE methyltransferases methylate specifically this position in a mechanism that requires an S‐adenosyl‐L‐methionine (AdoMet) molecule as cofactor. Here we report the structure of Apo and AdoMet‐bound Lpg2936 from Legionella pneumophila at 1.5 and 2.3 Å, respectively. The protein comprises an N‐terminal PUA domain and a C‐terminal SPOUT domain. The latter is responsible for protein dimerization and cofactor binding. Comparison with similar structures suggests that Lpg2936 is an RsmE‐like enzyme that can target the equivalent of U1498 in the L. pneumophila ribosomal RNA, thereby potentially enhancing ribosomal activity during infection‐mediated effector production. The multiple copies of the enzyme found in both structures reveal a flexible conformation of the bound AdoMet ligand. Isothermal titration calorimetry measurements suggest an asymmetric two site binding mode. Our results therefore also provide unprecedented insights into AdoMet/RsmE interaction, furthering our understanding of the RsmE catalytic mechanism.
Highlights
RNA methylation is an important modification of the ribosome responsible for modulating ribosomal activity
The methylation of U1498 located in the 16S ribosomal RNA of Escherichia coli is an important modification affecting ribosomal activity
Based on amino-acid sequence conservation, MTases can be grouped into functional classes such as the ribosomal RNA small subunit methyltransferase A (RsmA) class for the methylation of the m62A1518 and m62A1519, the RsmB class for m5C967, the RsmC for m2G1207, or the RsmE class for the methylation of the m3U1498.2,6
Summary
RNA methylation is an important modification of the ribosome responsible for modulating ribosomal activity. Methylation of specific bases in the ribosome subunits alters ribosomal RNA (rRNA) folding and interactions with specific proteins, resulting in global changes in levels of protein synthesis.[1] The transfer of methyl groups to acceptor RNAs is catalyzed by RNA methyltransferases (MTases), enzymes that use S-adenosyl-L-methionine (AdoMet or SAM) molecules as a source of methyl groups. Based on amino-acid sequence conservation, MTases can be grouped into functional classes such as the ribosomal RNA small subunit methyltransferase A (RsmA) class for the methylation of the m62A1518 and m62A1519, the RsmB class for m5C967, the RsmC for m2G1207, or the RsmE class for the methylation of the m3U1498 (numbering according to the E. coli 16S rRNA).[2,6] Methylation of U1498 has been shown to impact on ribosomal function and fidelity. U1498 together with other bases in ribosomal RNA helix 44 where U1498 is located have been shown to be involved in hygromycin B binding, supporting a role in the response to antibiotics.[7]
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