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, Inho Lee, Huyen Thi Tran, Bookyo Sur, Seunghwan Kim, Jeong Gu Kim, Yeh Jin Ahn, Sun Shin Cha, Lin Woo Kang

Research output: Contribution to journalArticlepeer-review

10 Scopus citations

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 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.

Original languageEnglish
Pages (from-to)7307-7314
Number of pages8
JournalJournal of Agricultural and Food Chemistry
Volume64
Issue number39
DOIs
StatePublished - 5 Oct 2016

Keywords

  • Xanthomonas oryzae pv. oryzae
  • bacterial blight
  • fragment chemical
  • peptide deformylase
  • pesticide

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