Crystal Structures of Peptide Deformylase from Rice Pathogen Xanthomonas oryzae pv. oryzae in Complex with Substrate Peptides, Actinonin, and Fragment Chemical Compounds

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.

Synthesis of N-Methylmorpholinium Derivatives Possessing a 1,3,4-Oxadiazole Core as Feasible Antibacterial Agents against Plant Bacterial Diseases

“…erefore, novel and safe frameworks with highly efficient bioactivity should be urgently excavated and developed [20][21][22][23].…”

Synthesis, Biological Activity and Action Mechanism Study of Novel Chalcone Derivatives Containing Malonate

“…oryzae (Xoo) is an excessive albinism that occurs during any rice growth period. In the case of the occurrence and spread of this disease, it may result in a substantial reduction of production by up to 80 % . Ralstonia solanacearum (Rs) bacterial wilt is the most important bacterial disease that damages tobacco, and important cash crops such as tobacco, tomato, peanut and potato are seriously damaged .…”

Antibiotic activities of propanolamine containing 1,4-benzoxazin-3-ones against phytopathogenic bacteria

“…[3][4][5][6] Currently, only a few established commercial bactericides, namely, bismerthiazol (BT), etridiazole, benthiazole and thiodiazole copper (TC), are used for the treatment of these plant bacterial diseases. Unfortunately, longterm use of these antimicrobial agents has resulted in the emergence of antimicrobial resistance in many of these pathogenic bacteria, [7][8][9] so the discovery of new antibiotics that elicit their antimicrobial activity through novel modes of action is very important. 10,11 Recently, 1,4-benzoxazin-3-one derivatives have gained increasing attention because of their broad pharmacological activities, including examples that display antibacterial, 12,13 antifungal, 14,15 herbicidal, 16,17 anticancer, 18,19 neurodegenerative diseases 20 and platelet aggregation inhibitor activities.…”

“… 3–6 Currently, only a few established commercial bactericides, namely, bismerthiazol (BT), etridiazole, benthiazole and thiodiazole copper (TC), are used for the treatment of these plant bacterial diseases. Unfortunately, long-term use of these antimicrobial agents has resulted in the emergence of antimicrobial resistance in many of these pathogenic bacteria, 7–9 so the discovery of new antibiotics that elicit their antimicrobial activity through novel modes of action is very important. 10,11 …”