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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
journal contribution
posted on 2016-09-12, 00:00 authored by 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 KangXanthomonas
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.
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Peptide deformylaseSubstrate Peptidessubstrate-binding pocketcrystal structuresXoPDF1.9 Å resolutionFragment Chemical Compounds Xanthomonas oryzae pvrice cultivationPDF inhibitor actinonin-bound structurefragment chemical moleculesfragment chemical compoundsXoo PDFPeptide DeformylaseRice Pathogen Xanthomonas oryzae pvformyl groupfragment chemical-bound structurescrystal Structures
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