Interaction of the tRNA-derived unusual nucleoside, t6A, with Mn(II) and Mg(II)

Functional anticodon architecture of human tRNALys3 includes disruption of intraloop hydrogen bonding by the naturally occurring amino acid modification, t6A

The structure of the human tRNA(Lys3) anticodon stem and loop domain (ASL(Lys3)) provides evidence of the physicochemical contributions of N6-threonylcarbamoyladenosine (t(6)A(37)) to tRNA(Lys3) functions. The t(6)A(37)-modified anticodon stem and loop domain of tRNA(Lys3)(UUU) (ASL(Lys3)(UUU)- t(6)A(37)) with a UUU anticodon is bound by the appropriately programmed ribosomes, but the unmodified ASL(Lys3)(UUU) is not [Yarian, C., Marszalek, M., Sochacka, E., Malkiewicz, A., Guenther, R., Miskiewicz, A., and Agris, P. F., Biochemistry 39, 13390-13395]. The structure, determined to an average rmsd of 1.57 +/- 0.33 A (relative to the mean structure) by NMR spectroscopy and restrained molecular dynamics, is the first reported of an RNA in which a naturally occurring hypermodified nucleoside was introduced by automated chemical synthesis. The ASL(Lys3)(UUU)-t(6)A(37) loop is significantly different than that of the unmodified ASL(Lys3)(UUU), although the five canonical base pairs of both ASL(Lys3)(UUU) stems are in the standard A-form of helical RNA. t(6)A(37), 3'-adjacent to the anticodon, adopts the form of a tricyclic nucleoside with an intraresidue H-bond and enhances base stacking on the 3'-side of the anticodon loop. Critically important to ribosome binding, incorporation of the modification negates formation of an intraloop U(33).A(37) base pair that is observed in the unmodified ASL(Lys3)(UUU). The anticodon wobble position U(34) nucleobase in ASL(Lys3)(UUU)-t(6)A(37) is significantly displaced from its position in the unmodified ASL and directed away from the codon-binding face of the loop resulting in only two anticodon bases for codon binding. This conformation is one explanation for ASL(Lys3)(UUU) tendency to prematurely terminate translation and -1 frame shift. At the pH 5.6 conditions of our structure determination, A(38) is protonated and positively charged in ASL(Lys3)(UUU)-t(6)A(37) and the unmodified ASL(Lys3)(UUU). The ionized carboxylic acid moiety of t(6)A(37) possibly neutralizes the positive charge of A(+)(38). The protonated A(+)(38) can base pair with C(32), but t(6)A(37) may weaken the interaction through steric interference. From these results, we conclude that ribosome binding cannot simply be an induced fit of the anticodon stem and loop, otherwise the unmodified ASL(Lys3)(UUU) would bind as well as ASL(Lys3)(UUU)-t(6)A(37). t(6)A(37) and other position 37 modifications produce the open, structured loop required for ribosomal binding.

Metal binding ability of hypermodified nucleosides of t-RNA. Potentiometric and spectroscopic studies on the metal complexes of N-[(9-beta-D-ribofuranosylpurin-6-yl)-carbamoyl] threonine

Copper(II), nickel(II), zinc(II), manganese(II), and magnesium(II) complexes of t6A (N-[9-beta-D-ribofuranosylpurin-6-yl)carbamoyl] threonine and t6Ade (N6(threoninocarbonyl)adenine) were studied by potentiometric and spectroscopic methods. It was found that t6Ade has three dissociable protons in the accessible pH range (N1 and N9 of purine and carboxylate), while only two pK values are characteristic of t6A. Magnesium(II) and manganese(II) do not interact effectively with these ligands, but copper(II) and nickel(II) ions form very stable complexes with the coordination of purine N1, deprotonated amide nitrogen, and carboxylate oxygen donors.

Magnesium ion inner sphere complex in the anticodon loop of phenylalanine transfer ribonucleic acid

The binding of Ca2+ and Mg2+ to tRNAPhe is analyzed by equilibrium titrations and temperature-jump measurements using the Wye base fluorescence as a label. Titration experiments starting with the folded structure of the tRNA (high salt and low temperature) show that Ca2+ and Mg2+ binding detected by Wye base fluorescence changes is associated with equilibrium constants between 1 x 10(3) and 3 x 10(3) M-1. The binding of Ca2+ leads to an increase of the relaxation time associated with a conformation change of the anticodon loop and to a decrease of the corresponding amplitude. These data are represented quantitatively by a two-step reaction scheme with a preferential binding of Ca2+ to one of the anticodon conformations. When Mg2+ is added, an extra relaxation process is observed with time constants around 1 ms. This process demonstrates the formation of a Mg2+ inner sphere complex. Relaxation time constants and amplitudes are represented quantitatively by a three-step reaction scheme. Mg2+ binds preferentially to one of the anticodon conformations. In the absence of Mg2+, these conformations are populated almost equally with a transition rate constant around 5 x 10(3) s-1. The Mg2+ inner sphere complex is formed with a relatively low rate constant of (1--2) x 10(3) s-1, indicating a conformational barrier. These data strongly suggest that the Mg2+ site analyzed in the present investigation corresponds to the anticodon site with a distorted octahedral coordination characterized by X-ray analysis. The results are discussed in terms of the anticodon function and also with respect to their implications upon Mg2+ binding to nucleic acids in general.