Functional and structural analysis of HviXyn11D xylanase from Hypocrea virens and its application to xylooligosaccharide production from agro-food by-products.
Aug 2026· International Journal of Biological Macromolecules· Vol 380, pp.
153966
· 0 citations· 75 references
Medicine
Abstract
Xylanases play important roles in lignocellulosic biomass degradation and have broad industrial applications. The discovery of new xylanases expands our understanding of these enzymes and provides new opportunities for industrial applications. This study performed biochemical and structural characterization of the xylanase Xyn11D from Hypocrea virens (HviXyn11D) and evaluated its potential for XOS production from agro-food by-products. HviXyn11D exhibited optimal hydrolytic activity against beechwood xylan at 50 °C and pH 5. Its enzymatic activity was enhanced in the presence of the biomass-derived compounds furfural, 5-hydroxymethylfurfural, and vanillin. The crystal structure of HviXyn11D exhibited a typical β-jelly roll fold and showed a unique substrate-binding cleft compared with homologous xylanases, adopting a closed conformation of the substrate-binding cleft with rigid thumb and finger domains. Molecular dynamics simulations demonstrated that higher temperatures increased the flexibility of the thumb and finger domains, leading to an open conformation of the substrate-binding cleft. Recombinant HviXyn11D enabled the hydrolysis of agro-biomass by-products derived from rice straw, corn cob, and sugarcane bagasse, resulting in successful XOS production. Together, these findings highlight the potential industrial applications of HviXyn11D in biomass degradation and provide new insights into the molecular and structural functions of HviXyn11D and the GH11 xylanase family.
This work offers the first molecular insight into P. eryngii xylanases, highlighting PeXyn1 for agro-waste valorization and multiivalent interactions at the CBM1-catalytic interface restrict structural fluctuations, promoting a stable conformation.
Xiaohang Li, Xian-Feng Du, Yan Zhang et al.· Journal of Agricultural and...· 0 citations
Lignocellulosic biomass has significant potential as a renewable feedstock for the production of biofuels and bioproducts. However, its structural complexity, particularly the crystalline nature of cellulose and protective lignin matrix, poses considerable challenges for enzymatic degradation. Fungi isolated from diverse lignocellulosic wastes, particularly olive pomace in Morocco, are a significant, yet underutilized resource of lignocellulolytic enzymes with a potential to overcome these challenges.
This study investigated the structural and functional properties of lignocellulolytic enzymes derived from 9 filamentous fungi. A total of 80 curated sequences were systematically categorized into cellulases and ligninases. Phylogenetic analysis was conducted on representative endoglucanases, β-glucosidases, and laccases to assess their diversity. Physicochemical parameters, secondary structure content, and thermostability indices were determined using ExPASy ProtParam and SOPMA. Homology models were generated with SWISS-MODEL and validated through PROCHECK, ERRAT, and ProSA. Molecular docking with AutoDock was used to evaluate the interactions of β-glucosidase with cellobiose.
Phylogenetic analysis revealed high evolutionary diversity among the examined species. Several enzymes showed favorable aliphatic indices and GRAVY scores, suggesting thermostability and hydrophilicity. β-Glucosidase from Fusarium equiseti showed the strongest predicted binding energy to cellobiose (–5.32 kcal/mol), with hydrogen bonding mediated by key residues, including Asp88, Arg94, Lys185, Gln197, Asp276, and Gln278, at optimal distances (1.95–2.58 Å).
This integrative in silico study highlights the predictive potential of Moroccan fungal β-glucosidases, particularly from F. equiseti, for future applications in lignocellulose bioconversion.
Arif Soukaina, Mouna Janati, M. Benaddou et al.· BioTechnologia· 0 citations
The high-resolution crystal structure of TsaGH11 provided a better understanding of the molecular mechanism of TsaGH11 and offer valuable guidance for the rational engineering of GH11 xylanases for industrial applications.
Ki Hyun Nam· International Journal of Mol...· 0 citations
Mannans are abundant plant hemicelluloses, and endo-β-mannanases are important biocatalysts for their conversion into functional manno-oligosaccharides. Here, we report the structural and functional characterization of a glycoside hydrolase family 134 β-mannanase from Aspergillus nidulans (AnGH134) and a structure-guided engineering strategy to improve its performance on locust bean gum. The 1.75 Å crystal structure reveals the conserved lysozyme-like fold of GH134 enzymes and supports an inverting catalytic mechanism with Glu43 and Asp55 as the putative catalytic residues. Docking, mutational, and molecular dynamics analyses indicate that AnGH134 uses an extended substrate-binding groove and that groove-exit residues and the C-terminal region contribute to productive catalysis. Guided by these findings, N-terminal fusion of CBM10 enhanced catalytic efficiency and thermal stability, whereas C-terminal fusion was detrimental. These results provide a framework for engineering GH134 mannanases.
Sheng-Chia Chen, Po-Chih Kuo, Wen-Ming Chen et al.· Journal of Agricultural and...· 0 citations
Straw return is widely used to enhance soil organic matter in black soil regions; however, low temperatures severely constrain the microbial degradation of straw. In this study, a wild fungal strain Talaromyces stipitatus with robust hydrolytic activity under cold conditions was isolated from black soil. A xylanase, TsTA1, secreted by this fungus, was shown to be active at low temperatures. Through molecular engineering, a series of TsTA1 mutants were generated, and three variants, M142Y, I161V, and F215Y, were demonstrated have substantially (1.5 to 2-fold) increased catalytic efficiency compared to the wild-type enzyme. Structural analyses indicated that the M142Y and F215Y substitutions enhance activity by introducing additional hydrogen bonding with the substrate. Interestingly, the I161V mutation markedly altered the pH range in which the enzyme is active, conferring alkaline pH tolerance. These findings enhance the understanding of straw decomposition by cold-adapted microbes and demonstrate a successful strategy for improving enzyme performance under challenging environmental conditions.
Da-Lin Zhou, Xi-Yang Wang, Wen-Li Li et al.· Bioresource Technology· 0 citations
Efficient xylose bioconversion is limited by the catalytic performance of xylulokinase (XylB), which phosphorylates d-xylulose to xylulose-5-phosphate. This study aimed to improve XylB from Lactococcus lactis N8 using a multi-dimensional semi-rational design strategy integrating sequence conservation, structure-based screening, mutagenesis, molecular docking, and molecular dynamics simulations. Asn301 was identified as a key functional hotspot, and Met259 was found to modulate the active-site hydrophobic environment. Combinatorial mutagenesis generated two superior variants, XylBM259H/N301G and XylBM259H/N301H, with more than 200% higher specific activity than the wild-type XylB (XylBWT) while retaining stable expression and environmental adaptability. Mechanistic analyses showed strengthened ATP binding, improved d-xylulose positioning, enhanced ligand affinity, and balanced local flexibility with structural compactness. These findings provide efficient XylB variants and a transferable strategy for engineering lignocellulose-related enzymes.
Ya-Qian Ai, Tao Geng, Wen-Jie Chen et al.· Journal of Agricultural and...· 0 citations
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