Unusual anticodon loop structure found in E.coli lysine tRNA

Although both tRNA^Lya and tRNA^Glu of tRNA^Lya possess similar anticodon loop sequences, with the same hypermodifled nucleoside 5-methylaminomethyl-2-thiouridine (mnm⁵8²U) at the first position of their anticodons, the anticodon loop structures of these two tRNAs containing the modified nucleoside appear to be quite different as judged from the following observations. (1) The CD band derived from the mnm⁵s²U residue is negative for tRNA^Glu, but positive for tRNA^Lya. (2) The mnm⁵s²U monomer itself and the mnm⁵s²U-containing anticodon loop fragment of tRNA^Lya show the same negative CD bands as that of tRNA^Glu. (3) The positive CD band of tRNA^Lya changes to negative when the temperature is raised. (4) The reactivity of the mnm⁵s²U residue toward H₂O₂ is much lower for tRNA^Lya than for tRNA^Glu. These features suggest that tRNA^Lya has an unusual anticodon loop structure, in which the mnm⁵s²U residue takes a different conformation from that of tRNA^Glu; whereas the mnm⁵s²U base of tRNA^Glu has no direct bonding with other bases and is accessible to a solvent, that of tRNA^Lya exists as if in some way buried in its anticodon loop. The limited hydrolysis of both tRNAs by various RNases suggests that some differences exist in the higher order structures of tRNA^Lya and tRNA^Glu. The Influence of the unusual anticodon loop structure observed for tRNA^Lya on its function in the translational process is also discussed.