engleski

Evolutionary relationships of seryl-tRNA synthetases based on 3D modeling

Background and purpose: The specific attachment of amino acids to the 3' end of tRNA is a key reaction in protein biosynthesis. It is catalyzed, in general, by 20 aminoacyl-tRNA synthetases (aaRS), structurally very diverse family of enzymes. For many years we have been studying the mechanism of serylation, employed by seryl-tRNA synthetases from different organisms and/or cellular compartments, by combination of protein engineering and genetic approaches. Since none of the eukaryal SerRSs have yet been crystallized, we are using protein 3D models to place our results in a structural context. In this work we show the importance of 3D models in phylogenetic analyses. Materials and methods: The rigid body superposition method was used to compare 3D structural models of various seryl-tRNA synthetases in order to infer their phylogenetic relationships. Results: The distance matrix was constructed for the selected region (involving the active site domains) of 21 seryl-tRNA synthetases modeled upon the coordinates of the crystallized Thermus thermophilus enzyme. This was used for the construction of a 3D based phylogenetic tree, which follows the overall topologies of sequence based phylogenies. The results of structure-based phylogeny inference were used to estimate the quality of the models. Conclusion: Phylogenetic analyses based on modeled protein structures can yield biologically meaningful results, despite the limited accuracy of the models.

seryl-tRNA synthetase; 3D structure; protein structure modeling; evolution

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