Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of bacterial blight of rice, one of the most devastating rice diseases. We analysed the time-resolved transcriptional expression of aminoacyl-tRNA synthetase (aaRS) genes in Xoo cells treated with rice-leaf extract. Most aaRS genes showed decreased expression in the initial 30 min and recovered or increased expression in the later 30 min. The protein-synthetic machinery of bacterial cells is an important target for developing antibiotic agents; aaRSs play an essential role in peptide synthesis by attaching amino acids onto the corresponding tRNA. In bacteria, glutaminyl-tRNA (Gln-tRNA^Gln) is synthesised in two steps by glutamyl-tRNA synthetase (GluRS) and tRNA-dependent aminotransferase, the indirect biosynthetic mechanism of which is not present in eukaryotes. We determined the crystal structure of GluRS from Xoo (XoGluRS) at resolution of 3.0 Å, this being the first GluRS structure from a plant pathogen such as Xoo. The XoGluRS structure consists of five domains, which are conserved in other bacterial GluRS structures. In the bacterial GluRS structures, the Rossmann-fold catalytic domain and the stem-contact domain are most conserved in both sequence and structure. The anticodon-binding domain 1 is less conserved in sequence but overall structure is conserved. The connective-polypeptide domain and the anticodon-binding domain 2 show various conformations in structure. The XoGluRS structure could provide useful information to develop a new pesticide against Xoo and bacterial blight.