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

Yıl 2023, Cilt: 20 Sayı: 1, 211 - 229, 19.01.2023

Yusuf Sürmeli

https://doi.org/10.33462/jotaf.1155764

Cited By: 3

Öz

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.

Anahtar Kelimeler

Thermoacidophilic xylanase, Molecular docking, GH11 xylanase, Animal feed additive, UniProt/TrEMBL database

Teşekkür

The author would like to thank Library and Documentation Department from Namık Kemal University for the contribution to the free access to the full-text articles.

Fungal Termoasidofilik GH11 Ksilanazlarının İn Siliko Filojeni, Dizi ve Yapı Analizleri

Öz

Termoasidofilik ksilanaz enzimleri, çoğunlukla hayvan yemi katkı maddesi olarak tercih edilmektedir. Bu çalışmada, çeşitli mantar türlerine ait altı termoasidofilik GH11 ksilanazın (Gymnopus androsaceus ksilanazı = GaXyl, Penicilliopsis zonata ksilanazı = PzXyl, Aspergillus neoniger ksilanazı = AnXyl, Calocera viscosa ksilanazı = CvXyl, Acidomyces richmondensis ksilanazı = ArXyl, Oidiodendron maius ksilanazı = OmXyl) in siliko filojeni, dizi, yapı ve enzim-docking kompleks analizleri gerçekleştirilmiştir. Bunu yapmak için, UniProt/TrEMBL veri tabanındaki gözden geçirilmemiş protein girdilerine ait altı mantar termoasidofilik GH11 ksilanazının amino asit dizileri moleküler filojeni ve dizi açısından araştırıldı. Ayrıca, üç boyutlu tahmini enzim modelleri oluşturuldu ve daha sonra çeşitli biyoinformatik programları kullanılarak hesaplamalı olarak doğrulandı. Enzim ve substrat arasındaki etkileşimler, iki substratın (ksilotetraoz = X4 ve ksilopentaoz = X5) varlığında docking programı aracılığıyla analiz edildi. Moleküler filojeni analizine göre, bu enzimlerin üç kümesi oluştu: birinci grup PzXyl, AnXyl ve CvXyl'e sahipti ve ikinci grup GaXyl ve OmXyl'e sahipti ve üçüncü grup ArXyl'i içeriyordu. Çoklu dizi hizalama analizi, beş ksilanazın (ArXyl, OmXyl, CvXyl, PzXyl, AnXyl) daha uzun N-terminal bölgelerine sahip olduğunu gösterdi, bu da GaXyl'e göre daha yüksek termal stabiliteye sahip olduklarını işaret etmiştir. Homoloji modelleme, tahmin edilen tüm model yapılarının büyük ölçüde korunduğunu gösterdi. Docking analizi sonuçları, CvXyl, OmXyl ve AnXyl'in GaXyl, PzXyl ve ArXyl ksilanazlara kıyasla iki substrata daha yüksek bağlanma verimliliğine sahip olduğunu ve CvXyl-X4 docking kompleksinin -9.8 kCal/mol'lük bir bağlanma enerjisiyle en yüksek substrat afinitesine sahip olduğunu gösterdi. CvXyl, OmXyl ve AnXyl enzimleri, daha düşük bağlanma verimliliğine sahip diğer enzimlerden farklı olarak, yaygın olarak B8 β-kolunda iki substrat ile etkileşime giren arjinin içeriyordu. Sonuç olarak, bu üç termoasidofilik ksilanaz enziminin hayvan yemi katkı maddesi olarak daha iyi adaylar olabileceği sonucuna varılmıştır.

Anahtar Kelimeler

Termoasidofilik ksilanaz, Moleküler yerleştirme, GH11 ksilanaz, Hayvan yem katkısı, UniProt/TrEMBL veritabanı

Kaynakça

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