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Elongation factor Tu (EF-Tu) exhibits significant specificity for the different elongator tRNA bodies in order to offset its variable affinity to the esterified amino acid. Three X-ray cocrystal structures reveal that while most of the contacts with the protein involve the phosphodiester backbone of tRNA, a single hydrogen bond is observed between the Glu390 and the amino group of a guanine in the 51–63 base pair in the T-stem of tRNA. Here we show that the Glu390Ala mutation of  Thermus thermophilus  EF-Tu selectively destabilizes binding of those tRNAs containing a guanine at either position 51 or 63 and that mutagenesis of the 51–63 base pair in several tRNAs modulates their binding affinities to EF-Tu. A comparison of  Escherichia coli  tRNA sequences suggests that this specificity mechanism is conserved across the bacterial domain. While this contact is an important specificity determinant, it is clear that others remain to be identified.

The 51–63 base pair of tRNA confers specificity for binding by EF-Tu