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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

Title
Crystal Structures of Peptide Deformylase from Rice Pathogen Xanthomonas oryzae pv. oryzae in Complex with Substrate Peptides, Actinonin, and Fragment Chemical Compounds
Authors
Ho-Phuong-Thuy NgoThien-Hoang HoLee, InhoHuyen-Thi TranSur, BookyoKim, SeunghwanKim, Jeong-GuAhn, Yeh-JinCha, Sun-ShinKang, Lin-Woo
Ewha Authors
차선신
SCOPUS Author ID
차선신scopus
Issue Date
2016
Journal Title
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
ISSN
0021-8561JCR Link1520-5118JCR Link
Citation
vol. 64, no. 39, pp. 7307 - 7314
Keywords
bacterial blightXanthomonas oryzae pv. oryzaepeptide deformylasepesticidefragment chemical
Publisher
AMER CHEMICAL SOC
Indexed
SCI; SCIE; SCOPUS WOS scopus
Abstract
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.
DOI
10.1021/acs.jafc.6b02976
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자연과학대학 > 화학·나노과학전공 > Journal papers
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