Bacterial toxin-antitoxin modules contribute to the stress adaptation, persistence, and dormancy of bacteria for survival under environmental stresses and are involved in bacterial pathogenesis. In Salmonella Typhimurium, the Gcn5-related N-acetyltransferase toxin TacT reportedly acetylates the a-amino groups of the aminoacyl moieties of several aminoacyl-tRNAs, inhibits protein synthesis, and promotes persister formation during the infection of macrophages. Here, we show that TacT exclusively acetylates Gly-tRNA Gly in vivo and in vitro. The crystal structure of the TacT:acetyl-Gly-tRNA Gly complex and the biochemical analysis reveal that TacT specifically recognizes the discriminator U73 and G71 in tRNA Gly , a combination that is only found in tRNA Gly isoacceptors, and discriminates tRNA Gly from other tRNA species. Thus, TacT is a Gly-tRNA Gly -specific acetyltransferase toxin. The molecular basis of the specific aminoacyl-tRNA acetylation by TacT provides advanced information for the design of drugs targeting Salmonella.