Bioinformatics Analysis of Nitrite Reducate from Pseudomonas aeruginosa HGP9 and the Structure Prediction with Homology Modeling

Nitrite reductase (nirS) is a key enzyme of denitrification catalyzing the one electron reduction of nitrite (NO₂^-) to nitrogen monoxide (NO).In this study, nirS gene was cloned from Pseudomonas aeruginosa HGP9 strain. The phylogenetic tree was constructed and the secondary structure was predicted by bioinformatics. Results showed that nirS gene was 99.8% similar to the nitrite reductase from Pseudomonas aeruginosa NCTC 6750 strain. Most of alpha-helices stretches are formed in the first 1/4 of the sequence and the beta-sheets are present in the last 3/4 sequences. Homology modeling based on using nitrite reductase (PDBID: 1gjqA ) as template for nirS indicated that two independent subunits comprised a homodimer in nirS crystal structure, and each monomer is composed of a c-heme domain and a d1-heme domain. both of them are cytochrom super family. Compared to the three-dimensional structure of nirS, there was a nature mutation in nirS that located the site residue of Phe109 in P. aeruginosa HGP9 strain (the residue was Thr84 in P. aeruginosa NCTC 6750 strain), and the mutation site was in the heme c domain.