Three Common Subunits in the Editing Domains of Class Ia tRNA Synthetases.

To identify conserved structural or functional subunit(s) in the CP1 (editing) domains of class Ia tRNA synthetases, five available structures were compared and analyzed. Through sequence alignments of the CP1 domains, three conserved regions were found near the amino acid binding site in the editing domain. Structural overlapping of the three subunits clearly showed that there exist three common structural subunits in all of the five editing RS structures. The new alignment suggests a translocation movement of the CP1 domain caused by the binding with tRNA. Based on the experimental and modeling results, it is proposed that subunits 1 and 3 accommodate the incoming amino acid binding, while subunit 2 contributes to the interactions with the adenosine ring of the A76 to stabilize the overall tRNA binding.. Since these subunits are critical for the editing reaction, we expect that these key structures should be conserved through all class Ia editing RSs.