Research Article

Crystallographic capture of a radical S-adenosylmethionine enzyme in the act of modifying tRNA

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Science  15 Apr 2016:
Vol. 352, Issue 6283, pp. 309-312
DOI: 10.1126/science.aad5367

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An RNA methylase caught in the act

RNA methylation is important in RNA function and in antibiotic resistance. The RNA methylase RlmN is a dual-specificity enzyme that can act on ribosomal and transfer RNA (tRNA). RlmN is a radical S-adenosylmethionine (SAM) enzyme, which produces a protein/RNA cross-linked intermediate. Schwalm et al. determined the structure of RlmN cross-linked to a tRNA substrate and found that the enzyme recognizes the overall shape of the tRNA. Then it remodels the anticodon region to access the base that it methylates. The remodeling activity is likely to be key to the enzyme's dual specificity.

Science, this issue p. 309


RlmN is a dual-specificity RNA methylase that modifies C2 of adenosine 2503 (A2503) in 23S rRNA and C2 of adenosine 37 (A37) in several Escherichia coli transfer RNAs (tRNAs). A related methylase, Cfr, modifies C8 of A2503 via a similar mechanism, conferring resistance to multiple classes of antibiotics. Here, we report the x-ray structure of a key intermediate in the RlmN reaction, in which a Cys118→Ala variant of the protein is cross-linked to a tRNAGlu substrate through the terminal methylene carbon of a formerly methylcysteinyl residue and C2 of A37. RlmN contacts the entire length of tRNAGlu, accessing A37 by using an induced-fit strategy that completely unfolds the tRNA anticodon stem-loop, which is likely critical for recognition of both tRNA and ribosomal RNA substrates.

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