Ngo, Ho-Phuong-Thuy Ho, Thien-Hoang Lee, Inho Tran, Huyen-Thi Sur, Bookyo Kim, Seunghwan Kim, Jeong-Gu Ahn, Yeh-Jin Cha, Sun-Shin Kang, Lin-Woo Crystal Structures of Peptide Deformylase from Rice Pathogen <i>Xanthomonas oryzae</i> pv. <i>oryzae</i> in Complex with Substrate Peptides, Actinonin, and Fragment Chemical Compounds <i>Xanthomonas oryzae</i> pv. <i>oryzae</i> (Xoo) causes bacterial blight on rice; this species is one of the most destructive pathogenic bacteria in rice cultivation worldwide. Peptide deformylase (PDF) catalyzes the removal of the <i>N</i>-formyl group from the N-terminus of newly synthesized polypeptides in bacterial cells and is an important target to develop antibacterial agents. We determined crystal structures of Xoo PDF (XoPDF) at up to 1.9 Å resolution, which include apo, two substrate-bound (methionine-alanine or methionine-alanine-serine), an inhibitor-bound (actinonin), and six fragment chemical-bound structures. Six fragment chemical compounds were bound in the substrate-binding pocket. The fragment chemical-bound structures were compared to the natural PDF inhibitor actinonin-bound structure. The fragment chemical molecules will be useful to design an inhibitor specific to XoPDF and a potential pesticide against Xoo. Peptide deformylase;Substrate Peptides;substrate-binding pocket;crystal structures;XoPDF;1.9 Å resolution;Fragment Chemical Compounds Xanthomonas oryzae pv;rice cultivation;PDF inhibitor actinonin-bound structure;fragment chemical molecules;fragment chemical compounds;Xoo PDF;Peptide Deformylase;Rice Pathogen Xanthomonas oryzae pv;formyl group;fragment chemical-bound structures;crystal Structures 2016-09-12
    https://acs.figshare.com/articles/journal_contribution/Crystal_Structures_of_Peptide_Deformylase_from_Rice_Pathogen_i_Xanthomonas_oryzae_i_pv_i_oryzae_i_in_Complex_with_Substrate_Peptides_Actinonin_and_Fragment_Chemical_Compounds/3846567
10.1021/acs.jafc.6b02976.s001