Abstract
Storage and directed transfer of information is the key requirement for the development of life. Yet any information stored on our genes is useless without its correct interpretation. The genetic code defines the rule set to decode this information. Aminoacyl-tRNA synthetases are at the heart of this process. We extensively characterize how these enzymes distinguish all natural amino acids based on the computational analysis of crystallographic structure data. The results of this meta-analysis show that the correct read-out of genetic information is a delicate interplay between the composition of the binding site, non-covalent interactions, error correction mechanisms, and steric effects.
Highlights
Based on all available structures in the Protein Data Bank (PDB), 424 (189 Class I, 235 Class II) three-dimensional structures of Aminoacyl-tRNA synthetases (aaRSs) co-crystallized with their corresponding amino acid ligands were analyzed
We investigated binding site geometry and cavity volume in order to quantify their potential contribution to amino acid recognition
The correct recognition of individual amino acids is a key determinant for evolutionary fitness of aaRSs and considered to be one of the major determinants for the closure of the genetic c ode[10]
Summary
Class I aaRSs show a strong conservation of hydrogen bonds with the primary amine group of the amino acid ligand with 83.16% of all structures forming this interaction. Interaction patterns with the backbone atoms of the amino acid ligand are strikingly consistent within Class II aaRSs. This class forms hydrogen bonds with the primary amine group in 92.15% of all structures.
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