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1.
Planta ; 259(5): 113, 2024 Apr 06.
Artigo em Inglês | MEDLINE | ID: mdl-38581452

RESUMO

MAIN CONCLUSION: Carbohydrates are hydrolyzed by a family of carbohydrate-active enzymes (CAZymes) called glycosidases or glycosyl hydrolases. Here, we have summarized the roles of various plant defense glycosidases that possess different substrate specificities. We have also highlighted the open questions in this research field. Glycosidases or glycosyl hydrolases (GHs) are a family of carbohydrate-active enzymes (CAZymes) that hydrolyze glycosidic bonds in carbohydrates and glycoconjugates. Compared to those of all other sequenced organisms, plant genomes contain a remarkable diversity of glycosidases. Plant glycosidases exhibit activities on various substrates and have been shown to play important roles during pathogen infections. Plant glycosidases from different GH families have been shown to act upon pathogen components, host cell walls, host apoplastic sugars, host secondary metabolites, and host N-glycans to mediate immunity against invading pathogens. We could classify the activities of these plant defense GHs under eleven different mechanisms through which they operate during pathogen infections. Here, we have provided comprehensive information on the catalytic activities, GH family classification, subcellular localization, domain structure, functional roles, and microbial strategies to regulate the activities of defense-related plant GHs. We have also emphasized the research gaps and potential investigations needed to advance this topic of research.


Assuntos
Glicosídeo Hidrolases , Polissacarídeos , Glicosídeo Hidrolases/química , Glicosídeo Hidrolases/metabolismo , Polissacarídeos/metabolismo , Carboidratos , Plantas/metabolismo , Glicosídeos/metabolismo
2.
Int J Biol Macromol ; 264(Pt 2): 130753, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38462094

RESUMO

Chitooligosaccharides (COS) possess versatile functional properties that have found extensive applications across various fields. Chitosanase can specifically hydrolyze ß-1,4 glycosidic bonds in chitosan to produce COS. In this study, Csn-PD, a glycoside hydrolase family 46 chitosanase from Paenibacillus dendritiformis, which produces (GlcN)2 as its main product, was rationally redesigned aiming to improve its catalytic performance. Based on the results of molecular docking analysis and multiple sequence alignment, four amino acid residues in Csn-PD (I101, T120, T220, and Y259) were pinpointed for targeted mutations. Beneficial mutations in terms of enhanced catalytic activity were then combined by site-directed mutagenesis. Notably, the most promising variant, Csn-PDT6 (Csn-PD I101M/T120E/T220G), exhibited an impressive eight-fold surge in activity compared to the wild-type Csn-PD. This heightened enzymatic activity was complemented by an enhanced pH stability profile. A compelling feature of Csn-PDT6 is its preservation of the hydrolytic product profile observed in Csn-PD. This characteristic further accentuates its candidacy for the targeted production of (GlcN)2. The success of our strategic approach is vividly illustrated by the significant improvements achieved in the catalytic performance of the chitosanase, encompassing both its activity and stability. These developments offer a valuable model that may have implications for the semi-rational design of other enzymes.


Assuntos
Quitosana , Paenibacillus , Simulação de Acoplamento Molecular , Glicosídeo Hidrolases/química , Quitosana/química , Hidrólise
3.
Int J Biol Macromol ; 265(Pt 1): 130993, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38508567

RESUMO

Hemicellulases are enzymes that hydrolyze hemicelluloses, common polysaccharides in nature. Thermophilic hemicellulases, derived from microbial strains, are extensively studied as natural biofuel sources due to the complex structure of hemicelluloses. Recent research aims to elucidate the catalytic principles, mechanisms and specificity of hemicellulases through investigations into their high-temperature stability and structural features, which have applications in biotechnology and industry. This review article targets to serve as a comprehensive resource, highlighting the significant progress in the field and emphasizing the vital role of thermophilic hemicellulases in eco-friendly catalysis. The primary goal is to improve the reliability of hemicellulase enzymes obtained from thermophilic bacterial strains. Additionally, with their ability to break down lignocellulosic materials, hemicellulases hold immense potential for biofuel production. Despite their potential, the commercial viability is hindered by their high enzyme costs, necessitating the development of efficient bioprocesses involving waste pretreatment with microbial consortia to overcome this challenge.


Assuntos
Bactérias , Biocombustíveis , Reprodutibilidade dos Testes , Glicosídeo Hidrolases/química , Lignina
4.
Int J Biol Macromol ; 265(Pt 2): 131131, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38527679

RESUMO

Glycoside hydrolases (GHs) are industrially important enzymes that hydrolyze glycosidic bonds in glycoconjugates. In this study, we found a GH3 ß-glucosidase (CcBgl3B) from Cellulosimicrobium cellulans sp. 21 was able to selectively hydrolyze the ß-1,6-glucosidic bond linked glucose of ginsenosides. X-ray crystallographic studies of the ligand complex ginsenoside-specific ß-glucosidase provided a novel finding that support the catalytic mechanism of GH3. The substrate was clearly identified within the catalytic center of wild-type CcBgl3B, revealing that the C1 atom of the glucose was covalently bound to the Oδ1 group of the conserved catalytic nucleophile Asp264 as an enzyme-glycosyl intermediate. The glycosylated Asp264 could be identified by mass spectrometry. Through site-directed mutagenesis studies with Asp264, it was found that the covalent intermediate state formed by Asp264 and the substrate was critical for catalysis. In addition, Glu525 variants (E525A, E525Q and E525D) showed no or marginal activity against pNPßGlc; thus, this residue could supply a proton for the reaction. Overall, our study provides an insight into the catalytic mechanism of the GH3 enzyme CcBgl3B.


Assuntos
Glicosídeo Hidrolases , beta-Glucosidase , Raios X , Hidrólise , Modelos Moleculares , beta-Glucosidase/química , Glicosídeo Hidrolases/química , Glucose/metabolismo , Catálise , Cristalografia por Raios X , Especificidade por Substrato
5.
J Agric Food Chem ; 72(8): 4358-4366, 2024 Feb 28.
Artigo em Inglês | MEDLINE | ID: mdl-38349745

RESUMO

The hydrolytic products of chitosanase from Streptomyces avermitilis (SaCsn46A) were found to be aminoglucose and chitobiose, whereas those of chitosanase from Bacillus subtilis (BsCsn46A) were chitobiose and chitotriose. Therefore, the sequence alignment between SaCsn46A and BsCsn46A was conducted, revealing that the structure of BsCsn46A possesses an extra loop region (194N-200T) at the substrate binding pocket. To clarify the impact of this loop on hydrolytic properties, three mutants, SC, TJN, and TJA, were constructed. Eventually, the experimental results indicated that SC changed the ratio of chitobiose to chitotriose hydrolyzed by chitosanase from 1:1 into 2:3, while TJA resulted in a ratio of 15:7. This experiment combined molecular research to unveil a crucial loop within the substrate binding pocket of chitosanase. It also provides an effective strategy for mutagenesis and a foundation for altering hydrolysate composition and further applications in engineering chitosanase.


Assuntos
Bacillus subtilis , Quitosana , Bacillus subtilis/genética , Bacillus subtilis/metabolismo , Polimerização , Glicosídeo Hidrolases/química , Alinhamento de Sequência
6.
Int J Biol Macromol ; 262(Pt 2): 130089, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38360236

RESUMO

Brevicoryne brassicae, an aphid species, exclusively consumes plants from the Brassicaceae family and employs a sophisticated defense mechanism involving a myrosinase enzyme that breaks down glucosinolates obtained from its host plants. In this work, we employed combined quantum mechanical and molecular mechanical (QM/MM) calculations and molecular dynamics (MD) simulations to study the catalytic reaction of aphid myrosinase. A proper QM region to study the myrosinase reaction should contain the whole substrate, models of Gln-19, His-122, Asp-124, Asn-166, Glu-167, Lys-173, Tyr-180, Val-228, Tyr-309, Tyr-346, Ile-347, Glu-374, Glu-423, Trp-424, and a water molecule. The calculations show that Asp-124 and Glu-423 must be charged, His-122 must be protonated on NE2, and Glu-167 must be protonated on OE2. Our model reproduces the anomeric retaining characteristic of myrosinase and indicates that the deglycosylation reaction is the rate-determining step of the reaction. Based on the calculations, we propose a reaction mechanism for aphid myrosinase-mediated hydrolysis of glucosinolates with an overall barrier of 15.2 kcal/mol. According to the results, removing a proton from Arg-312 or altering it to valine or methionine increases glycosylation barriers but decreases the deglycosylation barrier.


Assuntos
Afídeos , Animais , Sequência de Aminoácidos , Glucosinolatos , Glicosídeo Hidrolases/química
7.
Biosci Biotechnol Biochem ; 88(5): 538-545, 2024 Apr 22.
Artigo em Inglês | MEDLINE | ID: mdl-38331414

RESUMO

Bacterial α-1,3-glucanase, classified as glycoside hydrolase (GH) family 87, has been divided into 3 subgroups based on differences in gene sequences in the catalytic domain. The enzymatic properties of subgroups 1 and 3 of several bacteria have been previously investigated and reported; however, the chemical characterization of subgroup 2 enzymes has not been previously conducted. The α-1,3-glucanase gene from Paenibacillus alginolyticus NBRC15375 (PaAgl) belonging to subgroup 2 of GH family 87 was cloned and expressed in Escherichia coli. PgAgl-N1 (subgroup 3) and PgAgl-N2 (subgroup 1) from P. glycanilyticus NBRC16188 were expressed in E. coli, and their enzymatic characteristics were compared. The amino acid sequence of PaAgl demonstrated that the homology was significantly lower in other subgroups when only the catalytic domain was compared. The oligosaccharide products of the mutan-degrading reaction seemed to have different characteristics among subgroups 1, 2, and 3 in GH family 87.


Assuntos
Sequência de Aminoácidos , Clonagem Molecular , Escherichia coli , Expressão Gênica , Glicosídeo Hidrolases , Paenibacillus , Paenibacillus/enzimologia , Paenibacillus/genética , Glicosídeo Hidrolases/genética , Glicosídeo Hidrolases/química , Glicosídeo Hidrolases/metabolismo , Escherichia coli/genética , Especificidade por Substrato , Proteínas Recombinantes/genética , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Domínio Catalítico , Concentração de Íons de Hidrogênio , Oligossacarídeos/metabolismo
8.
Enzyme Microb Technol ; 175: 110410, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38340378

RESUMO

Prunin of desirable bioactivity and bioavailability can be transformed from plant-derived naringin by the key enzyme α-L-rhamnosidase. However, the production was limited by unsatisfactory properties of α-L-rhamnosidase such as thermostability and organic solvent tolerance. In this study, biochemical characteristics, and hydrolysis capacity of a novel α-L-rhamnosidase from Spirochaeta thermophila (St-Rha) were investigated, which was the first characterized α-L-rhamnosidase for Spirochaeta genus. St-Rha showed a higher substrate specificity towards naringin and exhibited excellent thermostability and methanol tolerance. The Km of St-Rha in the methanol cosolvent system was decreased 7.2-fold comparing that in the aqueous phase system, while kcat/Km value of St-Rha was enhanced 9.3-fold. Meanwhile, a preliminary conformational study was implemented through comparative molecular dynamics simulation analysis to explore the mechanism underlying the methanol tolerance of St-Rha for the first time. Furthermore, the catalytic ability of St-Rha for prunin preparation in the 20% methanol cosolvent system was explored, and 200 g/L naringin was transformed into 125.5 g/L prunin for 24 h reaction with a corresponding space-time yield of 5.2 g/L/h. These results indicated that St-Rha was a novel α-L-rhamnosidase suitable for hydrolyzing naringin in the methanol cosolvent system and provided a better alternative for improving the efficient production yield of prunin.


Assuntos
Florizina/análogos & derivados , Spirochaeta , Metanol , Glicosídeo Hidrolases/química , Solventes
9.
Int J Biol Macromol ; 262(Pt 2): 129783, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38280706

RESUMO

While hundreds of starch- and glycogen-degrading enzymes have been characterized experimentally in historical families such as GH13, GH14, GH15, GH57 and GH126 of the CAZy database (www.cazy.org), the α-amylase from Bacillus circulans is the only enzyme that has been characterized in family GH119. Since glycosidase families have been shown to often group enzymes with different substrates or products, a single characterized enzyme in a family is insufficient to extrapolate enzyme function based solely on sequence similarity. Here we report the rational exploration of family GH119 through the biochemical characterization of five GH119 members. All enzymes shared single α-amylase specificity but display distinct product profile. We also report the first kinetic constants in family GH119 and the first experimental validation of previously predicted catalytic residues in family GH119, confirming that families GH119 and GH57 can be grouped in the novel clan GH-T of the CAZy database.


Assuntos
Amido , alfa-Amilases , Humanos , Sequência de Aminoácidos , alfa-Amilases/química , Glicogênio , Glicosídeo Hidrolases/química , Especificidade por Substrato
10.
Biotechnol Lett ; 46(2): 201-211, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38280177

RESUMO

OBJECTIVES: Apiosidases are enzymes that cleave the glycosidic bond between the monosaccharides linked to apiose, a branched chain furanose found in the cell walls of vascular plants and aquatic monocots. There is biotechnological interest in this enzyme group because apiose is the flavor-active compound of grapes, fruit juice, and wine, and the monosaccharide is found to be a plant secondary metabolite with pharmaceutical properties. However, functional and structural studies of this enzyme family are scarce. Recently, a glycoside hydrolase family member GH140 was isolated from Bacteroides thetaiotaomicron and identified as an endo-apiosidase. RESULTS: The structural characterization and functional identification of a second GH140 family enzyme, termed MmApi, discovered through mangrove soil metagenomic approach, are described. Among the various substrates tested, MmApi exhibited activity on an apiose-containing oligosaccharide derived from the pectic polysaccharide rhamnogalacturonan-II. While the crystallographic model of MmApi was similar to the endo-apiosidase from Bacteroides thetaiotaomicron, differences in the shape of the binding sites indicated that MmApi could cleave apioses within oligosaccharides of different compositions. CONCLUSION: This enzyme represents a novel tool for researchers interested in studying the physiology and structure of plant cell walls and developing biocatalytic strategies for drug and flavor production.


Assuntos
Microbiota , Polissacarídeos , Oligossacarídeos/química , Glicosídeo Hidrolases/genética , Glicosídeo Hidrolases/química , Monossacarídeos
11.
Protein Expr Purif ; 217: 106432, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38232795

RESUMO

Natural ginsenoside needs to be converted into rare ginsenoside before it can be readily absorbed into the bloodstream for action. In this study, an α-l-arabinofuranosidase (α-l-AFase) gene Bsafs2 was cloned from Bacillus subtilis (B. subtilis). Bsafs2 was ligated to the expression vector pET28a(+), and the expression vector was constructed and transformed into Escherichia coli (E. coli) BL21 heterologous recombinant expression to obtain α-l-AFase. α-l-AFase can hydrolyze at the C20 site of Ginsenoside Rc to obtain rare ginsenoside Rd. Studies on the enzymatic property showed that α-l-AFase had good tolerance to ethanol, glucose, and l-arabinose. The optimum temperature of α-l-AFase was 40 °C and pH = 5.5. Kinetic parameters Km of α-l-AFase for pNPαAraf and Ginsenoside Rc were 1.93 and 8.9 mmol/L, the Vmax were 26 and 154 µmol/min/mg, the Kcat were 24.14 and 1.48 S-1, respectively. This study provides the enzyme source for the biotransformation of Ginsenoside Rc.


Assuntos
Ginsenosídeos , Ginsenosídeos/metabolismo , Bacillus subtilis/genética , Bacillus subtilis/metabolismo , Clonagem Molecular , Proteínas Recombinantes/química , Escherichia coli/metabolismo , Glicosídeo Hidrolases/química
12.
N Biotechnol ; 80: 1-11, 2024 May 25.
Artigo em Inglês | MEDLINE | ID: mdl-38163476

RESUMO

Polysaccharide Utilization Loci (PULs) are physically linked gene clusters conserved in the Gram-negative phylum of Bacteroidota and are valuable sources for Carbohydrate Active enZyme (CAZyme) discovery. This study focuses on BD-ß-Gal, an enzyme encoded in a metagenomic PUL and member of the Glycoside Hydrolase family 154 (GH154). BD-ß-Gal showed exo-ß-galactosidase activity with regiopreference for hydrolyzing ß-d-(1,6) glycosidic linkages. Notably, it exhibited a preference for d-glucopyranosyl (d-Glcp) over d-galactopyranosyl (d-Galp) and d-fructofuranosyl (d-Fruf) at the reducing end of the investigated disaccharides. In addition, we determined the high resolution crystal structure of BD-ß-Gal, thus providing the first structural characterization of a GH154 enzyme. Surprisingly, this revealed an (α/α)6 topology, which has not been observed before for ß-galactosidases. BD-ß-Gal displayed low structural homology with characterized CAZymes, but conservation analysis suggested that the active site was located in a central cavity, with conserved E73, R252, and D253 as putative catalytic residues. Interestingly, BD-ß-Gal has a tetrameric structure and a flexible loop from a neighboring protomer may contribute to its reaction specificity. Finally, we showed that the founding member of GH154, BT3677 from Bacteroides thetaiotaomicron, described as ß-glucuronidase, displayed exo-ß-galactosidase activity like BD-ß-Gal but lacked a tetrameric structure.


Assuntos
Carboidratos , Glicosídeo Hidrolases , Glicosídeo Hidrolases/química , Domínio Catalítico , Polissacarídeos , beta-Galactosidase , Especificidade por Substrato , Cristalografia por Raios X
13.
J Agric Food Chem ; 72(2): 1302-1320, 2024 Jan 17.
Artigo em Inglês | MEDLINE | ID: mdl-38175162

RESUMO

Inulin is widely used as a prebiotic and emerging as a priming compound to counteract plant diseases. We isolated inulin-degrading strains from the lettuce phyllosphere, identified as Bacillus subtilis and Priestia megaterium, species hosting well-known biocontrol organisms. To better understand their varying inulin degradation strategies, three intracellular ß-fructofuranosidases from P. megaterium NBRC15308 were characterized after expression in Escherichia coli: a predicted sucrose-6-phosphate (Suc6P) hydrolase (SacAP1, supported by molecular docking), an exofructanase (SacAP2), and an invertase (SacAP3). Based on protein multiple sequence and structure alignments of bacterial glycoside hydrolase family 32 enzymes, we identified conserved residues predicted to be involved in binding phosphorylated (Suc6P hydrolases) or nonphosphorylated substrates (invertases and fructanases). Suc6P hydrolases feature positively charged residues near the structural catalytic pocket (histidine, arginine, or lysine), whereas other ß-fructofuranosidases contain tryptophans. This correlates with our phylogenetic tree, grouping all predicted Suc6P hydrolases in a clan associated with genomic regions coding for transporters involved in substrate phosphorylation. These results will help to discriminate between Suc6P hydrolases and other ß-fructofuranosidases in future studies and to better understand the interaction of B. subtilis and P. megaterium endophytes with sucrose and/or fructans, sugars naturally present in plants or exogenously applied in the context of defense priming.


Assuntos
Inulina , Fosfatos Açúcares , beta-Frutofuranosidase , beta-Frutofuranosidase/genética , beta-Frutofuranosidase/metabolismo , Inulina/metabolismo , Filogenia , Simulação de Acoplamento Molecular , Glicosídeo Hidrolases/química , Sacarose/metabolismo , Bactérias/genética , Bactérias/metabolismo
14.
Int J Biol Macromol ; 256(Pt 2): 128416, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38029919

RESUMO

Polysaccharide hydrolases are enzymes capable of hydrolyzing polysaccharides to generate oligosaccharides that have diverse applications in the food, feed and pharmaceutical industries. However, the detailed mechanisms governing the compositions of their hydrolysates remain poorly understood. Previously, we identified a novel neopullulase Amy117, which exclusively converts pullulan to panose by specifically cleaving α-1,4-glycosidic bonds. Yet, several enzymes with high homology to Amy117 produce a mixture of glucose, maltose and panose during pullulan hydrolysis. To explore this particular phenomenon, we compared the sequences and structures between Amy117 and the maltose amylase ThMA, and identified a specific residue Thr299 in Amy117 (equivalent to His294 in ThMA) within the product-releasing cleft of Amy117, which might be responsible for this characteristic feature. Using structure-based rational design, we have successfully converted the product profiles of pullulan hydrolysates between Amy117 and ThMA by simply altering this key residue. Molecular docking analysis indicated that the key residue at the product-releasing outlet altered the product profile by affecting the panose release rate. Moreover, we modeled the long-chain pullulan substrate G8 to examine its potential conformations and found that G8 might undergo a conformational change in the narrow cleft that allows the Amy117 variant to specifically recognize α-1,6-glycosidic bonds.


Assuntos
Glicosídeo Hidrolases , Maltose , Glicosídeo Hidrolases/química , Simulação de Acoplamento Molecular , Amilases , Hidrólise , Especificidade por Substrato
15.
Proteins ; 92(2): 236-245, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-37818702

RESUMO

The subsequent biochemical and structural investigations of the purified recombinant α-l-rhamnosidase from Aspergillus oryzae expressed in Pichia pastoris, designated as rAoRhaA, were performed. The specific activity of the rAoRhaA wild-type was higher toward hesperidin and narirutin, where the l-rhamnose residue was α-1,6-linked to ß-d-glucoside, than toward neohesperidin and naringin with an α-1,2-linkage to ß-d-glucoside. However, no activity was detected toward quercitrin, myricitrin, and epimedin C. rAoRhaA kinetic analysis indicated that Km values for neohesperidin, naringin, and rutin were lower compared to those for hesperidin and narirutin. kcat values for hesperidin and narirutin were higher than those for neohesperidin, naringin, and rutin. High catalytic efficiency (kcat /Km ) toward hesperidin and narirutin was a result of a considerably high kcat value, while Km values for hesperidin and narirutin were higher than those for naringin, neohesperidin, and rutin. The crystal structure of rAoRhaA revealed that the catalytic domain was represented by an (α/α)6 -barrel with the active site located in a deep cleft and two ß-sheet domains were also present in the N- and C-terminal sites of the catalytic domain. Additionally, five asparagine-attached N-acetylglucosamine molecules were observed. The catalytic residues of AoRhaA were suggested to be Asp254 and Glu524, and their catalytic roles were confirmed by mutational studies of D254N and E524Q variants, which lost their activity completely. Notably, three aspartic acids (Asp117, Asp249, and Asp261) located at the catalytic pocket were replaced with asparagine. D117N variant showed reduced activity. D249N and D261N variants activities drastically decreased.


Assuntos
Aspergillus oryzae , Hesperidina , Aspergillus oryzae/genética , Aspergillus oryzae/metabolismo , Especificidade por Substrato , Cinética , Asparagina , Glicosídeo Hidrolases/química , Rutina , Glucosídeos
16.
Biosci Biotechnol Biochem ; 88(3): 276-282, 2024 Feb 21.
Artigo em Inglês | MEDLINE | ID: mdl-38066701

RESUMO

Plants synthesize large amounts of stored and structural polysaccharides. Aspergillus oryzae is used in traditional Japanese fermentation and produces many types of plant polysaccharide degradation-related enzymes. The carbohydrate-active enzymes of A. oryzae are important in the fermentation process and biotechnological applications. Because plant polysaccharides have a complex structure, cooperative and synergistic actions of enzymes are crucial for the degradation of plant polysaccharides. For example, the cooperative action of isoprimeverose-producing oligoxyloglucan hydrolase, ß-galactosidase, and α-xylosidase is important for the degradation of xyloglucan, and A. oryzae coordinates these enzymes at the expression level. In this review, I focus on the plant polysaccharide degradation-related enzymes identified in A. oryzae.


Assuntos
Aspergillus oryzae , Aspergillus oryzae/metabolismo , Glicosídeo Hidrolases/química , Polissacarídeos/metabolismo
17.
J Agric Food Chem ; 71(48): 18898-18908, 2023 Dec 06.
Artigo em Inglês | MEDLINE | ID: mdl-38053504

RESUMO

Pullulanases are multidomain α-glucan debranching enzymes with one or more N-terminal domains (NTDs) including carbohydrate-binding modules (CBMs) and domains of unknown function (DUFs). To elucidate the roles of NTDs in Lactobacillus acidophilus NCFM pullulanase (LaPul), two truncated variants, Δ41-LaPul (lacking CBM41) and Δ(41+DUFs)-LaPul (lacking CBM41 and two DUFs), were produced recombinantly. LaPul recognized 1.3- and 2.2-fold more enzyme attack-sites on starch granules compared to Δ41-LaPul and Δ(41+DUFs)-LaPul, respectively, as measured by interfacial kinetics. Δ41-LaPul displayed markedly lower affinity for starch granules and ß-cyclodextrin (10- and >21-fold, respectively) in comparison to LaPul, showing substrate binding mainly stems from CBM41. Δ(41+DUFs)-LaPul exhibited a 12 °C lower melting temperature than LaPul and Δ41-LaPul, indicating that the DUFs are critical for LaPul stability. Notably, Δ41-LaPul exhibited a 14-fold higher turnover number (kcat) and 9-fold higher Michaelis constant (KM) compared to LaPul, while Δ(41+DUFs)-LaPul's values were close to those of LaPul, possibly due to the exposure of aromatic by truncation.


Assuntos
Glicosídeo Hidrolases , Lactobacillus acidophilus , Humanos , Lactobacillus acidophilus/genética , Lactobacillus acidophilus/metabolismo , Glicosídeo Hidrolases/química , Glucanos/metabolismo , Amido/metabolismo
18.
ACS Chem Biol ; 18(12): 2564-2573, 2023 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-38051515

RESUMO

GH127 and GH146 microorganismal retaining ß-l-arabinofuranosidases, expressed by human gut microbiomes, feature an atypical catalytic domain and an unusual mechanism of action. We recently reported that both Bacteroides thetaiotaomicron BtGH146 and Bifidobacterium longum HypBA1 are inhibited by ß-l-arabinofuranosyl cyclophellitol epoxide, supporting the action of a zinc-coordinated cysteine as a catalytic nucleophile, where in most retaining GH families, an aspartate or glutamate is employed. This work presents a panel of ß-l-arabinofuranosyl cyclophellitol epoxides and aziridines as mechanism-based BtGH146/HypBA1 inhibitors and activity-based probes. The ß-l-arabinofuranosyl cyclophellitol aziridines both inhibit and label ß-l-arabinofuranosidase efficiently (however with different activities), whereas the epoxide-derived probes favor BtGH146 over HypBA1. These findings are accompanied by X-ray structural analysis of the unmodified ß-l-arabinofuranosyl cyclophellitol aziridine in complex with both isozymes, which were shown to react by nucleophilic opening of the aziridine, at the pseudoanomeric carbon, by the active site cysteine nucleophile to form a stable thioether bond. Altogether, our activity-based probes may serve as chemical tools for the detection and identification of low-abundance ß-l-arabinofuranosidases in complex biological samples.


Assuntos
Aziridinas , Cisteína , Humanos , Glicosídeo Hidrolases/química , Aziridinas/química , Compostos de Epóxi
19.
Acta Crystallogr D Struct Biol ; 79(Pt 11): 1026-1043, 2023 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-37877949

RESUMO

Fucoidanases (EC 3.2.1.-) catalyze the hydrolysis of glycosidic bonds between fucose residues in fucoidans. Fucoidans are a compositionally and structurally diverse class of fucose-containing sulfated polysaccharides that are primarily found in brown seaweeds. Here, the structural characterization of a novel endo-α(1,4)-fucoidanase, Mef1, from the marine bacterium Muricauda eckloniae is presented, showing sequence similarity to members of glycoside hydrolase family 107. Using carbohydrate polyacrylamide gel electrophoresis and nuclear magnetic resonance analyses, it is shown that the fucoidanase Mef1 catalyzes the cleavage of α(1,4)-linkages between fucose residues sulfated on C2 in the structure [-3)-α-L-Fucp2S-(1,4)-α-L-Fucp2S-(1-]n in fucoidan from Fucus evanescens. Kinetic analysis of Mef1 activity by Fourier transform infrared spectroscopy revealed that the specific Mef1 fucoidanase activity (Uf) on F. evanescens fucoidan was 0.1 × 10-3 Uf µM-1. By crystal structure determination of Mef1 at 1.8 Šresolution, a single-domain organization comprising a (ß/α)8-barrel domain was determined. The active site was in an extended, positively charged groove that is likely to be designed to accommodate the binding of the negatively charged, sulfated fucoidan substrate. The active site of Mef1 comprises the amino acids His270 and Asp187, providing acid/base and nucleophile groups, respectively, for the hydrolysis of glycosidic bonds in the fucoidan backbone. Electron densities were identified for two possible Ca2+ ions in the enzyme, one of which is partially exposed to the active-site groove, while the other is very tightly coordinated. A water wire was discovered leading from the exterior of the Mef1 enzyme into the active site, passing the tightly coordinated Ca2+ site.


Assuntos
Flavobacteriaceae , Fucose , Cinética , Polissacarídeos/química , Glicosídeo Hidrolases/química , Flavobacteriaceae/metabolismo
20.
Extremophiles ; 27(3): 29, 2023 Oct 17.
Artigo em Inglês | MEDLINE | ID: mdl-37847305

RESUMO

The studies have revealed alkaline exoinulinase produced by haloalkaliphilic phototrophic bacteria Ectothiorhodospirea mobilis Al-2 for the first time. A new method for the isolation of a homogeneous exoinulinase from the culture broth was developed and the properties of this enzyme have been investigated. It was shown that specified exoinulinase in contrast to the studied exoinulinases produced by microorganisms exhibits catalytic activity at the wide range of pH (7.0-10) and a temperature (20-60 °C) with a maximum of the inulolitic activity at pH 9.0 and 50 °C. The studied exoinulinase possessing also invertase activity (I/S1.4) is a monomeric protein with molecular mass 57Kda, as well as Km and Vmax for inulin 3.8 mM/ml and 10 µmol/ml/min-1, respectively. The studies of the influence of different metal ions on enzyme activity have shown that Mn+2, Cu+2, Co+2, Mg+2, NaCl 5-7% promote relatively higher catalytic activity while Zn+2, Cu+2 and Fe+2 partially suppress the enzyme activity and Hg2+completely inactivates the enzyme.The formation of only fructose and glucose at the enzymatic hydrolysis of inulin confirms that the studied exoinulinase belongs to the exo-type of enzymes. The obtained results supplement our fundamental knowledge in biochemistry-enzymology, as well as the biodiversity of microorganisms expressing exoinulinase. The studied exoinulinase exhibits activity at salinity of the medium and can potentially be used in the biotechnology of inulin bioconversion into bioproducts under alkaline conditions.


Assuntos
Glicosídeo Hidrolases , Inulina , Inulina/química , Inulina/metabolismo , Glicosídeo Hidrolases/química , Temperatura , Bactérias/metabolismo
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