Thermodynamic and Kinetic Framework of Selenocysteyl-tRNASec Recognition by Elongation Factor SelB

SelB is a specialized translation elongation factor that delivers selenocysteyl-tRNA(Sec) (Sec-tRNA(Sec)) to the ribosome. Here we show that Sec-tRNA(Sec) binds to SelB.GTP with an extraordinary high affinity (K-d = 0.2 pM). The tight binding is driven enthalpically and involves the net formation of four ion pairs, three of which may involve the Sec residue. The dissociation of tRNA from the ternary complex SelB.GTP.Sec-tRNA(Sec) is very slow (0.3 h(-1)), and GTP hydrolysis accelerates the release of Sect-RNA(Sec) by more than a million-fold (to 240 s(-1)). The affinities of Sec-tRNA(Sec) to SelB in the GDP or apoforms, or Ser-tRNA(Sec) and tRNA(Sec) to SelB in any form, are similar (K-d = 0.5 mu M). Thermodynamic coupling in binding of Sec-tRNA(Sec) and GTP to SelB ensures at the same time the specificity of Sec-versus Ser-tRNA(Sec) selection and rapid release of Sec-tRNA(Sec) from SelB after GTP cleavage on the ribosome. SelB provides an example for the evolution of a highly specialized protein-RNA complex toward recognition of unique set of identity elements. The mode of tRNA recognition by SelB is reminiscent of another specialized factor, eIF2, rather than of EF-Tu, the common delivery factor for all other aminoacyl-tRNAs, in line with a common evolutionary ancestry of SelB and eIF2.