In Silico Phylogeny, Sequence and Structure Analyses of Fungal Thermoacidophilic GH11 Xylanases

Abstract

Thermoacidophilic xylanase enzymes are mostly preferred for use as animal feed additives. In this study, we performed in silico phylogeny, sequence, structure, and enzyme-docked complex analyses of six thermoacidophilic GH11 xylanases belonging to various fungal species (Gymnopus androsaceus xylanase = GaXyl, Penicilliopsis zonata xylanase = PzXyl, Aspergillus neoniger xylanase = AnXyl, Calocera viscosa xylanase = CvXyl, Acidomyces richmondensis xylanase = ArXyl, Oidiodendron maius xylanase = OmXyl). To do this, amino acid sequences of six fungal thermoacidophilic GH11 xylanases, belonging to unreviewed protein entries in the UniProt/TrEMBL database, were investigated at molecular phylogeny and amino acid sequence levels. In addition, three-dimensional predicted enzyme models were built and then validated by using various bioinformatics programs computationally. The interactions between enzyme and the substrate were analyzed via docking program in the presence of two substrates (xylotetraose = X4 and xylopentaose = X5). According to molecular phylogeny analysis, three clusters of these enzymes occurred: the first group had PzXyl, AnXyl, and CvXyl, and the second group possessed GaXyl and OmXyl, and the third group included ArXyl. Multiple sequence alignment analysis demonstrated that the five xylanases (ArXyl, OmXyl, CvXyl, PzXyl, AnXyl) had longer N-terminal regions, indicating greater thermal stability, relative to the GaXyl. Homology modeling showed that all the predicted model structures were, to a great extent, conserved. Docking analysis results indicated that CvXyl, OmXyl, and AnXyl had higher binding efficiency to two substrates, compared to the GaXyl, PzXyl, and ArXyl xylanases, and CvXyl-X4 docked complex had the highest substrate affinity with a binding energy of -9.8 kCal/mol. CvXyl, OmXyl, and AnXyl enzymes commonly had arginine in B8 β-strand interacted with two substrates, different from the other enzymes having lower binding efficiency. As a result, it was concluded that the three thermoacidophilic xylanase enzymes might be better candidates as the animal feed additive.