Conformation and possible role of hypermodified nucleosides adjacent to 3'-end of anticodon in tRNA: N-(purin-6-ylcarbamoyl)-L-threonine riboside

The crystal structure of N-(purin-6-ylcarbamoyl)-L-threonine riboside was determined from three-dimensional x-ray diffraction data. The N⁶-substituent is distal ($\text{trans}$) to the imidazole ring, leading to a bifurcated hydrogen interaction involving two intramolecular contacts with the hydrogen on N(threonine): a hydrogen bond to N(1) of adenine and a close contact to the hydroxyl oxygen of threonine. The conformation of the molecule and the internal hydrogen bond completely block the two sites N⁶-H and N¹ of adenine from taking part in the Watson-Crick base pairing. This inability to base pair according to the Watson-Crick scheme appears as a common structural feature in all modified bases adjacent to the 3′-end of anticodons. These results, along with Crick's hypothesis for codon recognition, suggest that the hypermodified bases adjacent to the anticodons may be important in (i) preventing the misreading of the codons by bases adjacent to anticodons and (ii) promoting a single stranded conformation for the anticodon loops.