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There are about 20 aminoacyl-tRNA synthetases, one for each amino acid. Each aminoacyl-tRNA synthetase has a binding site that recognizes a specific amino acid, and other binding areas that recognize a particular tRNA through unique identity sites at the acceptor stem and/or anticodon loop of the tRNA.

When there are different tRNAs for the same amino acid, the aminoacyl-tRNA synthetase that recognizes a specific amino acid must also recognize the set of tRNAs that can be charged with that amino acid. Given that all tRNAs have different anticodons, how does the enzyme achieve the aforementioned task?

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    $\begingroup$ ncbi.nlm.nih.gov/books/NBK22356/#_A4154_ $\endgroup$ – canadianer Jun 24 '17 at 15:42
  • $\begingroup$ like you already said: each aminoacly-tRNA synthetase has 'binding areas that recognize a particular tRNA through unique identity sites at the acceptor stem and/or anticodon loop of the tRNA' - the anticodons only thing that are needed/used for the recognition $\endgroup$ – Nicolai Jun 24 '17 at 16:18
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You give the answer in your question:

binding areas that recognize a particular tRNA through unique identity sites at the acceptor stem and/or anticodon loop of the tRNA.

The point is that aminoacyl-tRNA synthetases that recognize tRNAs with different anticodons have to supplement any partial codon recognition with recognition of common features elsewhere, in particular the anticodon loop. Unfortunately this has evolved on a case-by-case basis and there is no simple ‘code’ one can refer to.

Thus, Berg et al. (Chapter 29), in discussing threonyl-tRNA synthetase, write (my emphasis):

As expected, the CCA arm extends into the zinc-containing activation site, where it is well positioned to accept threonine from threonyl adenylate. The enzyme interacts extensively not only with the acceptor stem of the tRNA, but also with the anticodon loop. The interactions with the anticodon loop are particularly revealing. The bases within the sequence CGU of the anticodon each participate in hydrogen bonds with the enzyme; those in which G and U take part appear to be more important because the C can be replaced by G or U with no loss of acylation efficiency.

The four codons for Thr are ACN, so in this case recognition of two bases of the anticodon will identify all tRNAs.

A diagram from Berg et al. showing the multiple interactions in threonine tRNA-synthatase is shown below.

Threonine tRNA synthetase

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  • $\begingroup$ Hi David, thank you for your answer. I was wondering, when different codons code for the same amino acid, it is because these codons differ in the 3rd base, not the first. So wouldn't the interactions between the first 2 bases of the tRNA anticodon be more important than the 3rd base? I am operating under the assumption that each enzyme recognizes a specific amino acid, and the set of tRNAs which the amino acid is supposed to be attached to, but the anticodons of this set of tRNAs differ in the 3rd base. $\endgroup$ – Jonathan Smith Jun 25 '17 at 1:47
  • $\begingroup$ @JonathanSmith — The confusion here is caused by using first and third, rather than 5' and 3'. Thus the codons for threonine are 5'-ACN-3' (with N, the ‘wobble’ base), whereas the tRNA anticodon that Berg et al. refer to is, in my opinion, best written 3'-UGC-5', so that the complementarity to the codon bases is evident. (Strictly they are correct to write CGU, as the direction is assumed to be 5' to 3', but in a text book every effort to make things clearer is appreciated by the reader.) $\endgroup$ – David Jun 25 '17 at 14:49

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