Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines

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One of the most prevalent base modifications involved in decoding is uridine 5-oxyacetic acid at the wobble position of tRNA. It has been known for several decades that this modification enables a single tRNA to decode all four codons in a degenerate codon box. We have determined structures of an anticodon stem-loop of tRNAVal containing the modified uridine with all four valine codons in the decoding site of the 30S ribosomal subunit. An intramolecular hydrogen bond involving the modification helps to prestructure the anticodon loop. We found unusual base pairs with the three noncomplementary codon bases, including a G·U base pair in standard Watson-Crick geometry, which presumably involves an enol form for the uridine. These structures suggest how a modification in the uridine at the wobble position can expand the decoding capability of a tRNA.

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Figure 1: The degeneracy of the genetic code.
Figure 2: cmo5U base-pairs with all four bases at the wobble position of the mRNA.
Figure 3: Comparison of cmo5U·G with standard U·G wobble.
Figure 4: The two pyrimidine-pyrimidine base pairs.

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We thank B. Sproat for help and advice on the polymer chemistry, W.D. Graham for purification and analysis of ASLVal, A. Kelley for purification and crystallization of 30S subunits, C.M. Dunham and S. Petry for help with synchrotron data collection, R. Ravelli, J. McCarthy and G. Leonard for help with data collection on beamline ID14 at the European Synchrotron Radiation Facility, and L. Passmore and M. Schmeing for helpful comments. This work was funded by the UK Medical Research Council (V.R.) and grants from the US National Institutes of Health (P.F.A. and V.R.), the US National Science Foundation (P.F.A.), the Agouron Institute (V.R.), the Austrian Academy of Sciences (A.W.) and the Polish Ministry of Science and Education (A.M.).

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Correspondence to Paul F Agris or V Ramakrishnan.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Derivatives of cmo5U. (PDF 59 kb)

Supplementary Fig. 2

Unbiased difference density for ribosomal A site. (PDF 113 kb)

Supplementary Fig. 3

Role of m6A37. (PDF 101 kb)

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Weixlbaumer, A., Murphy, F., Dziergowska, A. et al. Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines. Nat Struct Mol Biol 14, 498–502 (2007) doi:10.1038/nsmb1242

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