The crystal structure of Cys-tRNA^Cys–EF-Tu–GDPNP reveals general and specific features in the ternary complex and in tRNA

Abstract

Background: The translation elongation factor EF-Tu in its GTP-bound state forms a ternary complex with any aminoacylated tRNA (aa-tRNA), except initiator tRNA and selenocysteinyl-tRNA. This complex delivers aa-tRNA to the ribosomal A site during the elongation cycle of translation. The crystal structure of the yeast Phe-tRNA^Phe ternary complex with Thermus aquaticus EF-Tu–GDPNP (Phe-TC) has previously been determined as one representative of this general yet highly discriminating complex formation.

Results: The ternary complex of Escherichia coli Cys-tRNA^Cys and T. aquaticus EF-Tu–GDPNP (Cys-TC) has been solved and refined at 2.6 ° resolution. Conserved and variable features of the aa-tRNA recognition and binding by EF-Tu–GTP have been revealed by comparison with the Phe-TC structure. New tertiary interactions are observed in the tRNA^Cys structure. A ‘kissing complex’ is observed in the very close crystal packing arrangement.

Conclusions: The recognition of Cys-tRNA^Cys by EF-Tu–GDPNP is restricted to the aa-tRNA motif previously identified in Phe-TC and consists of the aminoacylated 3′ end, the phosphorylated 5′ end and one side of the acceptor stem and T stem. The aminoacyl bond is recognized somewhat differently, yet by the same primary motif in EF-Tu, which suggests that EF-Tu adapts to subtle variations in this moiety among all aa-tRNAs. New tertiary interactions revealed by the Cys-tRNA^Cys structure, such as a protonated C16:C59 pyrimidine pair, a G15:G48 ‘Levitt pair’ and an s⁴U8:A14:A46 base triple add to the generic understanding of tRNA structure from sequence. The structure of the ‘kissing complex’ shows a quasicontinuous helix with a distinct shape determined by the number of base pairs.