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Crystal Structures of Peptide Deformylase from Rice Pathogen Xanthomonas oryzae pv. oryzae in Complex with Substrate Peptides, Actinonin, and Fragment Chemical Compounds
- Crystal Structures of Peptide Deformylase from Rice Pathogen Xanthomonas oryzae pv. oryzae in Complex with Substrate Peptides, Actinonin, and Fragment Chemical Compounds
- Ho-Phuong-Thuy Ngo; Thien-Hoang Ho; Lee, Inho; Huyen-Thi Tran; Sur, Bookyo; Kim, Seunghwan; Kim, Jeong-Gu; Ahn, Yeh-Jin; Cha, Sun-Shin; Kang, Lin-Woo
- Ewha Authors
- SCOPUS Author ID
- Issue Date
- Journal Title
- JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
- 0021-8561; 1520-5118
- vol. 64, no. 39, pp. 7307 - 7314
- bacterial blight; Xanthomonas oryzae pv. oryzae; peptide deformylase; pesticide; fragment chemical
- AMER CHEMICAL SOC
- SCI; SCIE; SCOPUS
- Xanthomonas oryzae pv. oryzae (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 N-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 A 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.
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