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

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dc.contributor.authorSürmeli, Yusuf
dc.date.accessioned2023-05-06T17:23:41Z
dc.date.available2023-05-06T17:23:41Z
dc.date.issued2023
dc.departmentFakülteler, Ziraat Fakültesi, Tarımsal Biyoteknoloji Bölümü
dc.description.abstractThermoacidophilic 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 = X-4 and xylopentaose = X-5). 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-X-4 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 beta- 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.
dc.identifier.doi10.33462/jotaf.1155764
dc.identifier.endpage229
dc.identifier.issn1302-7050
dc.identifier.issn2146-5894
dc.identifier.issue1en_US
dc.identifier.scopus2-s2.0-85146941609
dc.identifier.scopusqualityQ3
dc.identifier.startpage211
dc.identifier.trdizinid1153692
dc.identifier.urihttps://doi.org/10.33462/jotaf.1155764
dc.identifier.urihttps://hdl.handle.net/20.500.11776/12245
dc.identifier.volume20
dc.identifier.wosWOS:000925798200020
dc.identifier.wosqualityN/A
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakTR-Dizin
dc.institutionauthorSürmeli, Yusuf
dc.language.isoen
dc.publisherUniv Namik Kemal
dc.relation.ispartofJournal Of Tekirdag Agriculture Faculty-Tekirdag Ziraat Fakultesi Dergisi
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccess
dc.subjectThermoacidophilic xylanase
dc.subjectMolecular docking
dc.subjectGH11 xylanase
dc.subjectAnimal feed additive
dc.subjectUniProt/TrEMBL database
dc.subjectTrichoderma-Reesei Endo-1,4-Beta-Xylanase-Ii
dc.subjectMicrobial Xylanases
dc.subjectProtein Sequences
dc.subjectWeb Server
dc.subjectEnzyme
dc.subjectCloning
dc.subjectEndo-Beta-1,4-Xylanase
dc.subjectCombination
dc.subjectExpression
dc.subjectResidues
dc.titleIn Silico Phylogeny, Sequence and Structure Analyses of Fungal Thermoacidophilic GH11 Xylanases
dc.typeArticle

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