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. 1978 Mar;5(3):893–903. doi: 10.1093/nar/5.3.893

Modified bases in tRNA: the structures of 5-carbamoylmethyl- and 5-carboxymethyl uridine.

H M Berman, D Marcu, P Narayanan
PMCID: PMC342031  PMID: 643621

Abstract

The crystal structures of two nucleosides, 5-carbamoylmethyluridine (1) and 5-carboxymethyluridine (2), were determined from three-dimensional x-ray diffraction data, and refined to R = 0.036 and R = 0.047, respectively. Compound 1 is in the C3'-endo conformation with chi +5.2 degrees (anti), psiinfinity = +63.4 degrees and psialpha = +180.0 degrees (tt); 2 is in the C2'endo conformation with chi +49.4 degrees (anti), psiinfinity -60.5 degrees and psialpha +60.0 degrees (gg). For each derivative, the plane of the side chain substituent is skewed with respect to the plane of the nucleobase; for 1, the carboxamide group is on the same side of the uracil plane vis a vis the ribose ring; for 2, the carboxyl group is on the opposite side of this plane. No base pairing is observed for either structure. Incorporation of structure 1 into a 3'-stacked tRNA anticodon appears to place 08 within hydrogen bonding distance of the 02' hydroxyl of ribose 33, which may limit the ability of such a molecule of tRNA to "wobble".

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Selected References

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