Structure and dynamics analysis of multi-domain putative β-1,4-glucosidase of family 3 glycoside hydrolase (PsGH3) from Pseudopedobacter saltans

Identification and Characterization of Two Novel Members of the Family Eubacteriaceae, Anaerofustis butyriciformans sp. nov. and Pseudoramibacter faecis sp. nov., Isolated from Human Feces

Members of Eubacteriaceae are involved in host health and diseases. Two Gram-stain-positive, strictly anaerobic, non-motile, non-spore-forming, and rod-shaped bacterial strains, HA2171T and HA2172T, were isolated from the feces of Chinese healthy donors. Based on 16S rRNA gene sequences, HA2171T and HA2172T belonged to the family Eubacteriaceae. Physiological and biochemical characterizations indicated that HA2171T and HA2172T were neutrophilic, mesophilic, and tolerant to low-concentration NaCl. The major cellular fatty acids (>10.0%) of HA2171T were C16:0, C14:0, C18:1ω7c, and C17:0 2-OH, and those of HA2172T were C14:0 and C16:0. MK-6 was the respiratory quinone in both strains. Phylogenetic and phylogenomic analyses showed that HA2171T was closest to Anaerofustis stercorihominis ATCC BAA-858T and that HA2172T as closest to Pseudoramibacter alactolyticus ATCC 23263T. Genome annotation revealed that the HA2171T and HA2172T were able to metabolize carbohydrates and produce acetate and butyrate. HA2172T contains genes associated with hydrogen sulfide production, which is a potential risk for diseases. Based on the phylogenetic, phenotypic, and chemotaxonomic characteristics, we propose that HA2171T and HA2172T represent two novel species, and the names Anaerofustis butyriciformans sp. nov. and Pseudoramibacter faecis sp. nov. are proposed.

Structural and functional insights into recombinant β-glucosidase from Thermothelomyces thermophilus: Cello-oligosaccharide hydrolysis and thermostability

β-glucosidases (BGLs) are key enzymes in the depolymerization of cellulosic biomass, catalyzing the conversion of cello-oligosaccharides into glucose. This conversion is pivotal for enhancing the production of second-generation ethanol or other value-added products in biorefineries. However, the process is often cost-prohibitive due to the high enzyme loadings required. Therefore, the discovery of new highly efficient BGLs represents a significant advancement. In this study, a BGL from the glycoside hydrolase family 3 (GH3) of the thermophilic fungus Thermothelomyces thermophilus (TthBgl3A) was heterologously expressed in Aspergillus nidulans. The recombinant enzyme exhibited optimal activity at pH 5.0 and 55 °C, with noteworthy stability for up to 160 h. A distinctive, extensive loop within the catalytic cavity of TthBgl3A facilitates hydrophobic interactions that enhance the binding and hydrolysis of long cello-oligosaccharides. Consequently, TthBgl3A has proven to be an efficient enzyme for the hydrolysis lignocellulosic biomass. These findings are significant for expanding the repertoire of enzymes produced by T. thermophilus and provide new insights into the potential application of TthBgl3A in the degradation of cellulosic materials and the production of valuable compounds.

Molecular dynamics-based structural insights of the first putative endoglucanase, PsGH5A of glycoside hydrolase family 5 from Pseudopedobacter saltans

CONTEXT

The putative endoglucanase, PsGH5A, from Pseudopedobacter saltans of family GH5 contains a catalytic module, PsGH5 (β/α)₈-TIM barrel), at N-terminal followed by a family 6 carbohydrate-binding module (CBM6, β-sandwich). Superposition of PsGH5A with PDB homologs revealed Glu220 and Glu318 as evolutionarily conserved and catalytic residues performing the hydrolysis through retaining-type mechanism, a canonical property of GH5 family. PsGH5A showed higher affinity for longer cellooligosaccharides, as long as cellodecaose with binding free energy (∆G) of - 13.72 kcal/mol upon the molecular docking, thereby indicating the endo-mode of hydrolysis. The radius of gyration, Rg (2.7 nm), and solvent accessible surface area, SASA (229.6 nm²), of PsGH5A-Cellotetraose complex were determined by MD simulation which was lower than that of PsGH5A (Rg, 2.8 nm, SASA, 267 nm²) demonstrating the compactness and affinity of PsGH5A with the cellulosic ligands. Cellulose compatibility of PsGH5A was further confirmed by MMPBSA and per-residue decomposition analysis, where notable ∆G of - 54.38 kcal/mol for PsGH5A-Cellotetraose complex was observed. Thus, PsGH5A could be potentially an efficient endoglucanase as it accommodated larger cellooligosaccharides at its active-site. PsGH5A is the first putative endoglucanase studied here from P. saltans which could be genome-mined for lignocellulosic biomass saccharification in the renewable energy sector.

METHODS

The 3-D structure of PsGH5A generated by AlphaFold2, RaptorX, SwissModel, Phyre2 and Robetta tool; YASARA was used for energy minimization of built models. UCLA SAVES-v6 was used for quality assessment of models. Molecular Docking was performed using SWISS-DOCK server and Chimera software. Molecular Dynamics simulations and MMPBSA analysis of PsGH5A and PsGH5A-Cellotetraose complex were performed on GROMACS 2019.6.