Crystal Structures of Peptide Deformylase from Rice Pathogen Xanthomonas oryzae pv. oryzae in Complex with Substrate Peptides, Actinonin, and Fragment Chemical Compounds.
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.
Department of Biological Sciences, Konkuk University , Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea.
Ho-Phuong-Thuy
HP
Ngo
Department of Biological Sciences, Konkuk University , Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea.
Thien-Hoang
TH
Ho
Department of Biological Sciences, Konkuk University , Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea.
Inho
I
Lee
Department of Biological Sciences, Konkuk University , Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea.
Huyen-Thi
HT
Tran
Department of Biological Sciences, Konkuk University , Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea.
Bookyo
B
Sur
Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA) , Jeonju 54874, Korea.
Seunghwan
S
Kim
Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA) , Jeonju 54874, Korea.
Jeong-Gu
JG
Kim
Department of Life Science, Sangmyung University , 7 Hongji-dong, Jongno-gu, Seoul 03016, Korea.
Yeh-Jin
YJ
Ahn
Department of Chemistry & Nano Science, Ewha Womans University , 52, Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Korea.
Sun-Shin
SS
Cha
Department of Biological Sciences, Konkuk University , Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea.
Lin-Woo
LW
Kang
D000581:Amidohydrolases / Q000737:chemistry*; D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins / Q000737:chemistry*; D018360:Crystallography, X-Ray; D015964:Gene Expression Regulation, Bacterial; D006877:Hydroxamic Acids / Q000737:chemistry; D012275:Oryza / Q000382:microbiology; D010455:Peptides / Q000737:chemistry; D010935:Plant Diseases / Q000382:microbiology; D013329:Structure-Activity Relationship; D014974:Xanthomonas / Q000201:enzymology*
D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D006877:Hydroxamic Acids; D010455:Peptides; D000581:Amidohydrolases; C084507:peptide deformylase; C010531:actinonin
Xanthomonas oryzae pv. oryzae; bacterial blight; fragment chemical; peptide deformylase; pesticide