Multiple rewards from a treasure trove of novel glycoside hydrolase and polysaccharide lyase structures: new folds, mechanistic details, and evolutionary relationships

Simulated Digestion and Fecal Fermentation Behaviors of Levan and Its Impacts on the Gut Microbiota

Levan is a microbial fructan widely explored in various fields owing to its excellent physical and biochemical properties. However, little is known about its digestion and fermentation characteristics in vitro. This study evaluated the potential prebiotic properties of levan obtained by enzymatic synthesis. Scanning electron microscopy, Fourier transform infrared spectroscopy, and nuclear magnetic resonance spectroscopy showed that the primary structures of levan remained stable after saliva-gastrointestinal digestion. The microtopography, molecular weight, and functional group of levan were seriously damaged during fecal fermentation. Moreover, the total short-chain fatty acid levels increased significantly, especially for propionic acid, butyric acid, and valeric acid. The 16S rDNA sequencing showed that levan mainly increased the abundance of Firmicutes; in genus levels, certain beneficial bacteria such as Megasphaera and Megamonas genera were remarkably promoted, and the proliferation of harmful genera was inhibited (such as Cedecea and Klebsiella). Overall, this study provided new insights into the potential probiotic mechanism of levan.

Chitosan Oligosaccharide Production Potential of Mitsuaria sp. C4 and Its Whole-Genome Sequencing

Chitooligosaccharide is a kind of functional food, which is the degradation product of chitosan (COS) catalyzed by the endo-chitosanase (COSE) enzyme. A COSE with a molecular weight of 34 kDa was purified and characterized from a newly isolated Mitsuaria sp. C4 (C4), and a 38.46% recovery rate and 4.79-fold purification were achieved. The purified C4 COSE exhibited optimum activity at 40°C and pH 7.2 and was significantly inhibited in the presence of Cu²⁺ and Fe³⁺. The K_m and V_min of the COSE toward COS were 2.449 g/L and 0.042 g/min/L, respectively. The highest COSE activity reached 8.344 U/ml after optimizing, which represented a 1.34-fold of increase. Additionally, chitooligosaccharide obtained by COSE hydrolysis of COS was verified by using thin-layer chromatography and high-performance liquid chromatography analysis. Whole-genome sequencing demonstrated that the C4 strain contains 211 carbohydrate enzymes, our purified COSE belonging to GHs-46 involved in carbohydrate degradation. Phylogenetic analysis showed that the novel COSE obtained from the C4 strain was clustered into the degree of polymerization = two to three groups, which can perform catalysis in a similar manner to produce (GlcN)₂ and (GlcN)₃. This work indicates that the C4 strain could be a good resource for enhancing carbohydrate degradation and might represent a useful tool for chitooligosaccharide production in the functional food industry.

Glycan utilization systems in the human gut microbiota: a gold mine for structural discoveries

The complex glycans comprising 'dietary fiber' evade the limited repertoire of human digestive enzymes and hence feed the vast community of microbes in the lower gastrointestinal tract. As such, complex glycans drive the composition of the human gut microbiota and, in turn, influence diverse facets of our nutrition and health. To access these otherwise recalcitrant carbohydrates, gut bacteria produce coordinated, substrate-specific arsenals of carbohydrate-active enzymes, glycan-binding proteins, oligosaccharide transporters, and transcriptional regulators. A recent explosion of biochemical and enzymological studies of these systems has led to the discovery of manifold new carbohydrate-active enzyme (CAZyme) families. Crucially underpinned by structural biology, these studies have also provided unprecedented molecular insight into the exquisite specificity of glycan recognition in the diverse CAZymes and non-catalytic proteins from the HGM. The revelation of a multitude of new three-dimensional structures and substrate complexes constitutes a 'gold rush' in the structural biology of the human gut microbiota.

Enhanced Azidolysis by the Formation of Stable Ser-His Catalytic Dyad in a Glycoside Hydrolase Family 10 Xylanase Mutant

Glycoside hydrolases require carboxyl groups as catalysts for their activity. A retaining xylanase from Streptomyces olivaceoviridis E-86 belonging to glycoside hydrolase family 10 possesses Glu128 and Glu236 that respectively function as acid/base and nucleophile. We previously developed a unique mutant of the retaining xylanase, N127S/E128H, whose deglycosylation is triggered by azide. A crystallographic study reported that the transient formation of a Ser–His catalytic dyad in the reaction cycle possibly reduced the azidolysis reaction. In the present study, we engineered a catalytic dyad with enhanced stability by site-directed mutagenesis and crystallographic study of N127S/E128H. Comparison of the Michaelis complexes of N127S/E128H with pNP-X₂ and with xylopentaose showed that Ser127 could form an alternative hydrogen bond with Thr82, which disrupts the formation of the Ser–His catalytic dyad. The introduction of T82A mutation in N127S/E128H produces an enhanced first-order rate constant (6 times that of N127S/E128H). We confirmed the presence of a stable Ser–His hydrogen bond in the Michaelis complex of the triple mutant, which forms the productive tautomer of His128 that acts as an acid catalyst. Because the glycosyl azide is applicable in the bioconjugation of glycans by using click chemistry, the enzyme-assisted production of the glycosyl azide may contribute to the field of glycobiology.

The molecular structure of the glycoside hydrolase domain of Cwp19 from Clostridium difficile

Clostridium difficile is a burden to healthcare systems around the world, causing tens of thousands of deaths annually. The S‐layer of the bacterium, a layer of protein found of the surface of cells, has received a significant amount of attention over the past two decades as a potential target to combat the growing threat presented by C. difficile infections. The S‐layer contains a wide range of proteins, each of which possesses three cell wall‐binding domains, while many also possess a “functional” region. Here, we present the high resolution structure of the functional region of one such protein, Cwp19 along with preliminary functional characterisation of the predicted glycoside hydrolase. Cwp19 has a TIM barrel fold and appears to possess a high degree of substrate selectivity. The protein also exhibits peptidoglycan hydrolase activity, an order of magnitude slower than that of lysozyme and is the first member of glycoside hydrolase‐like family 10 to be characterised. This research goes some way to understanding the role of Cwp19 in the S‐layer of C. difficile.

Database

Structural data are available in the PDB under the accession numbers 5OQ2 and 5OQ3.

Quantitative Kinetic Characterization of Glycoside Hydrolases Using High-Performance Anion-Exchange Chromatography (HPAEC)

High-performance anion-exchange chromatography coupled to pulsed amperometric detection (HPAEC-PAD) is a powerful analytical technique enabling the high-resolution separation and sensitive quantification of oligosaccharides. Here, we describe a general method for the determination of glycoside hydrolase kinetics that harnesses the intrinsic power of HPAEC-PAD to simultaneously monitor the release of multiple products under conditions of low substrate conversion. Thus, the ability to track product release under initial-rate conditions with substrate concentrations as low as 5 μM enables the determination of Michaelis-Menten kinetics for glycosidase activities, including hydrolysis and transglycosylation. This technique may also be readily extended to other carbohydrate-active enzymes (CAZymes), including polysaccharide lyases, and glycosyl transferases.

Performance of Hidden Markov Models in Recovering the Standard Classification of Glycoside Hydrolases

Glycoside hydrolases (GHs) are carbohydrate-active enzymes that assist the hydrolysis of glycoside bonds of complex sugars into carbohydrates. The current standard GH family classification is available in the CAZy database, which is based on the similarities of amino acid sequences and curated semi-automatically. However, with the exponential increase in data availability from genome sequences, automated classification methods are required for the fast annotation of coding sequences. Currently, the dbCAN database offers automatic annotations of signature domains from CAZy-defined classifications using a statistical approach, the hidden Markov models (HMMs). However, dbCAN does not contain the entire set of CAZy GH families. Moreover, no evaluation has been conducted so far of the viability of using HMM profiles as a means of automatically assigning GH amino acid sequences to the standard CAZy GH family classification itself. In this work, we performed a meta-analysis in which amino acid sequences from CAZy-defined GH families were used to build HMM family-specific profiles. We then queried a set with ~300 000 GH sequences against our database of HMM profiles estimated from CAZy families. We conducted the same evaluation against the available dbCAN HMM profiles. Our analyses recovered 65% of matches with the standard CAZy classification, whereas dbCAN HMMs resulted in 61% of matches. We also provided an analysis of the types of errors commonly found when HMMs are used to recover CAZy-based classifications. Although the performance of HMM was good, further developments are necessary for a fully automated classification of GH, allowing the standardization of GH classification among protein databases.

Structural Insight of a Trimodular Halophilic Cellulase with a Family 46 Carbohydrate-Binding Module

Cellulases are the key enzymes used in the biofuel industry. A typical cellulase contains a catalytic domain connected to a carbohydrate-binding module (CBM) through a flexible linker. Here we report the structure of an atypical trimodular cellulase which harbors a catalytic domain, a CBM46 domain and a rigid CBM_X domain between them. The catalytic domain shows the features of GH5 family, while the CBM46 domain has a sandwich-like structure. The catalytic domain and the CBM46 domain form an extended substrate binding cleft, within which several tryptophan residues are well exposed. Mutagenesis assays indicate that these residues are essential for the enzymatic activities. Gel affinity electrophoresis shows that these tryptophan residues are involved in the polysaccharide substrate binding. Also, electrostatic potential analysis indicates that almost the entire solvent accessible surface of CelB is negatively charged, which is consistent with the halophilic nature of this enzyme.

Combined inhibitor free-energy landscape and structural analysis reports on the mannosidase conformational coordinate

Mannosidases catalyze the hydrolysis of a diverse range of polysaccharides and glycoconjugates, and the various sequence-based mannosidase families have evolved ingenious strategies to overcome the stereoelectronic challenges of mannoside chemistry. Using a combination of computational chemistry, inhibitor design and synthesis, and X-ray crystallography of inhibitor/enzyme complexes, it is demonstrated that mannoimidazole-type inhibitors are energetically poised to report faithfully on mannosidase transition-state conformation, and provide direct evidence for the conformational itinerary used by diverse mannosidases, including β-mannanases from families GH26 and GH113. Isofagomine-type inhibitors are poor mimics of transition-state conformation, owing to the high energy barriers that must be crossed to attain mechanistically relevant conformations, however, these sugar-shaped heterocycles allow the acquisition of ternary complexes that span the active site, thus providing valuable insight into active-site residues involved in substrate recognition.