Modeling of PrnD protein from Pseudomonas fluorescens RajNB11 and its comparative structural analysis with PrnD proteins expressed in Burkholderia and Serratia

Abstract

Pyrrolnitrin is produced by Pseudomonas fluorescens and plays an important role in control of pathogenic fungi. The prnABCD gene cluster codes for enzymes involved in biosynthesis of pyrrolnitrin. Among the four genes, prnD is very important as it codes for arylamine N-oxygenase, the only biochemically characterized oxygenase involved in oxidation of the amino group of aminopyrrolnitrin to a nitro group to form pyrrolnitrin. A strain of Pseudomonas fluorescens RajNB11 efficient for antifungal activity was found to produce pyrrolnitrin. The prnD gene product of P. fluorescens RajNB11 that catalyzes the final step of production of pyrrolnitrin was characterized in the present study with regards to its stability and catalytic activity. The prnD gene was amplified from RajNB11, sequenced, translated, and 3-D modeled to its protein structure. The modeled protein of the test organism was compared to PrnD proteins of Burkholderia sp. and Serratia sp. The protein from P. fluorescens was found to be basic, hydrophilic with higher thermal stability, and easily separated after expression and purification. The protein of P. fluorescens was found to have a better folded structure, more serine residues in the active site, and better active site properties and isoelectric point value in comparison to PrnD proteins of Burkholderia and Serratia. Key word: Pseudomonas fluorescens, pyrrolnitrin, cloning, protein modeling