Asymmetric Evolution of Fidelity in Class IIa Aminoacyl-tRNA Synthetases: From Ancestral Promiscuity to Divergent Discrimination Mechanisms

Curated data and code supporting the manuscript "Asymmetric Evolution of Fidelity in Class IIa Aminoacyl-tRNA Synthetases: From Ancestral Promiscuity to Divergent Discrimination Mechanisms" (Journal of Molecular Evolution). Contains LUCA-proximal ancestral reconstructions of prolyl- and threonyl-tRNA synthetase and of the pre-duplication Class IIa ancestor AncSPT, the phylogenetic trees and alignments behind them, all 195 AlphaFold3 input specifications, the extracted pocket_ipTM binding metrics and competition ratios, AutoDock Vina and Amber MM-GBSA energy scores, molecular dynamics summary statistics for 27 trajectories, Pfam domain assignments, and the analysis and figure-generation code. Raw AlphaFold3 outputs and molecular dynamics trajectories are excluded for size and are available from the corresponding author on request; all values used in the manuscript are included here in reduced form.