Negative catalysis by the editing domain of class I aminoacyl-tRNA synthetases

Abstract The faithful protein synthesis is a vital property of the cell as errors in translation can diminish cellular fitness and lead to severe neurodegeneration. Aminoacyl-tRNA synthetases (AARS) translate the genetic code by loading tRNAs with the cognate amino acids. The errors in amino acid recognition are cleared at the AARS editing domain through hydrolysis of misaminoacyl-tRNAs. Here, using Escherichia coli isoleucyl-tRNA synthetase (IleRS) as a model enzyme, we showed that the editing domain of class I AARSs does not select for non-cognate amino acids that jeopardize the AARS fidelity. Instead, it selects against the cognate aminoacyl-tRNA providing a new paradigm wherein safeguarding against misediting constrains the editing evolution. The specificity is established by the residues that promote negative catalysis through destabilisation of the transition state comprising exclusively the cognate amino acid. Such error-correction design is powerful as it allows broad substrate acceptance of the editing domain along with its exquisite specificity in the non-error rejection. This is set up by in cis substrate delivery to the editing domain, a fingerprint of class I but not class II AARSs. However, we found a gap in this class rule by unveiling that class I IleRS releases misaminoacyl-tRNAIle and edits it in trans.