The Seryl-tRNA synthetase/tRNASer acceptor stem interface is mediated via a specific network of water molecules

• Published in: Biochemical and biophysical research communications 2011-09, Vol.412 (4), p.532-536
• Main Authors: Eichert, André, Oberthuer, Dominik, Betzel, Christian, Geßner, Reinhard, Erdmann, Volker A., Fürste, Jens P., Förster, Charlotte
• Format: Article
• Language: English
• Subjects: Binding Sites; Crystallography, X-Ray; Hydration; Nucleic Acid Conformation; Protein Conformation; RNA, Transfer, Ser - chemistry; Serine-tRNA Ligase - chemistry; Seryl-tRNA synthetase; Superposition experiments; tRNA-synthetase interaction; tRNASer; Water - chemistry
• ISSN: 0006-291X; 1090-2104
• DOI: 10.1016/j.bbrc.2011.07.030

► Seryl-tRNA synthetase aminoacylates tRNASer isoacceptors with the amino acid serine. ► The tRNASer identity elements are mainly located in the aminoacyl stem. ► Two tRNASer aminoacyl stem structures were superimposed to synthetase complex. ► The RNA/protein binding site is visualized with focus on the hydration pattern. tRNAs are aminoacylated by the aminoacyl-tRNA synthetases. There are at least 20 natural amino acids, but due to the redundancy of the genetic code, 64 codons on the mRNA. Therefore, there exist tRNA isoacceptors that are aminoacylated with the same amino acid, but differ in their sequence and in the anticodon. tRNA identity elements, which are sequence or structure motifs, assure the amino acid specificity. The Seryl-tRNA synthetase is an enzyme that depends on rather few and simple identity elements in tRNASer. The Seryl-tRNA-synthetase interacts with the tRNASer acceptor stem, which makes this part of the tRNA a valuable structural element for investigating motifs of the protein–RNA complex. We solved the high resolution crystal structures of two tRNASer acceptor stem microhelices and investigated their interaction with the Seryl-tRNA-synthetase by superposition experiments. The results presented here show that the amino acid side chains Ser151 and Ser156 of the synthetase are interacting in a very similar way with the RNA backbone of the microhelix and that the involved water molecules have almost identical positions within the tRNA/synthetase interface.