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1.
Int J Mol Sci ; 25(15)2024 Aug 05.
Article in English | MEDLINE | ID: mdl-39126103

ABSTRACT

The formation and analysis of amyloid fibers by two ß-glucosidases, BglA and BglB, belonging to the GH1 enzyme family, are reported. Both proteins have the (ß/α)8 TIM-barrel fold, which is characteristic of this family and is also the most common protein structure. BglA is an octamer, whereas BglB is a monomer. Amyloid fibrillation using pH and temperature as perturbing agents was investigated using fluorescence spectroscopy as a preliminary approach and corroborated using wide-field optical microscopy, confocal microscopy, and field-emission scanning electron microscopy. These analyses showed that both enzymes fibrillate at a wide range of acidic and alkaline conditions and at several temperature conditions, particularly at acidic pH (3-4) and at temperatures between 45 and 65 °C. Circular dichroism spectroscopy corroborated the transition from an α-helix to a ß-sheet secondary structure of both proteins in conditions where fibrillation was observed. Overall, our results suggest that fibrillation is a rather common phenomenon caused by protein misfolding, driven by a transition from an α-helix to a ß-sheet secondary structure, that many proteins can undergo if subjected to conditions that disturb their native conformation.


Subject(s)
Amyloid , Amyloid/chemistry , Amyloid/metabolism , Hydrogen-Ion Concentration , Glycoside Hydrolases/chemistry , Glycoside Hydrolases/metabolism , Circular Dichroism , Temperature , Protein Structure, Secondary , Protein Folding
2.
Carbohydr Polym ; 339: 122248, 2024 Sep 01.
Article in English | MEDLINE | ID: mdl-38823916

ABSTRACT

Arabinoxylan is a major hemicellulose in the sugarcane plant cell wall with arabinose decorations that impose steric restrictions on the activity of xylanases against this substrate. Enzymatic removal of the decorations by arabinofuranosidases can allow a more efficient arabinoxylan degradation by xylanases. Here we produced and characterized a recombinant Bifidobacterium longum arabinofuranosidase from glycoside hydrolase family 43 (BlAbf43) and applied it, together with GH10 and GH11 xylanases, to produce xylooligosaccharides (XOS) from wheat arabinoxylan and alkali pretreated sugarcane bagasse. The enzyme synergistically enhanced XOS production by GH10 and GH11 xylanases, being particularly efficient in combination with the latter family of enzymes, with a degree of synergism of 1.7. We also demonstrated that the enzyme is capable of not only removing arabinose decorations from the arabinoxylan and from the non-reducing end of the oligomeric substrates, but also hydrolyzing the xylan backbone yielding mostly xylobiose and xylose in particular cases. Structural studies of BlAbf43 shed light on the molecular basis of the substrate recognition and allowed hypothesizing on the structural reasons of its multifunctionality.


Subject(s)
Bifidobacterium longum , Cellulose , Endo-1,4-beta Xylanases , Glucuronates , Glycoside Hydrolases , Oligosaccharides , Saccharum , Xylans , Oligosaccharides/chemistry , Oligosaccharides/metabolism , Glycoside Hydrolases/metabolism , Glycoside Hydrolases/chemistry , Glucuronates/metabolism , Glucuronates/chemistry , Endo-1,4-beta Xylanases/metabolism , Endo-1,4-beta Xylanases/chemistry , Xylans/metabolism , Xylans/chemistry , Saccharum/chemistry , Saccharum/metabolism , Cellulose/chemistry , Cellulose/metabolism , Bifidobacterium longum/enzymology , Bifidobacterium longum/metabolism , Hydrolysis , Substrate Specificity , Recombinant Proteins/metabolism , Recombinant Proteins/chemistry , Disaccharides
3.
Int J Biol Macromol ; 269(Pt 1): 132036, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38697429

ABSTRACT

Alpha-glucosidase inhibitors play an important role in Diabetes Mellitus (DM) treatment since they prevent postprandial hyperglycemia. The Glycoside Hydrolase family 13 (GH13) is the major family of enzymes acting on substrates containing α-glucoside linkages, such as maltose and amylose/amylopectin chains in starch. Previously, our group identified glycoconjugate 1H-1,2,3-triazoles (GCTs) inhibiting two GH13 α-glycosidases: yeast maltase (MAL12) and porcine pancreatic amylase (PPA). Here, we combined kinetic studies and computational methods on nine GCTs to characterize their inhibitory mechanism. They all behaved as reversible inhibitors, and kinetic models encompassed noncompetitive and various mechanisms of mixed-type inhibition for both enzymes. Most potent inhibitors displayed Ki values of 30 µM for MAL12 (GPESB16) and 37 µM for PPA (GPESB15). Molecular dynamics and docking simulations indicated that on MAL12, GPESB15 and GPESB16 bind in a cavity adjacent to the active site, while on the PPA, GPESB15 was predicted to bind at the entrance of the catalytic site. Notably, despite its putative location within the active site, the binding of GPESB15 does not obstruct the substrate's access to the cleavage site. Our study contributes to paving the way for developing novel therapeutic strategies for managing DM-2 through GH13 α-glycosidases inhibition.


Subject(s)
Molecular Docking Simulation , Molecular Dynamics Simulation , Kinetics , Ligands , Swine , Glycoside Hydrolase Inhibitors/pharmacology , Glycoside Hydrolase Inhibitors/chemistry , Animals , Catalytic Domain , alpha-Glucosidases/metabolism , alpha-Glucosidases/chemistry , Glycoside Hydrolases/chemistry , Glycoside Hydrolases/metabolism , Glycoside Hydrolases/antagonists & inhibitors , Small Molecule Libraries/pharmacology , Small Molecule Libraries/chemistry , Triazoles/chemistry , Triazoles/pharmacology , Models, Molecular
4.
Biotechnol Lett ; 46(2): 201-211, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38280177

ABSTRACT

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.


Subject(s)
Microbiota , Polysaccharides , Oligosaccharides/chemistry , Glycoside Hydrolases/genetics , Glycoside Hydrolases/chemistry , Monosaccharides
5.
Int J Biol Macromol ; 242(Pt 1): 124734, 2023 Jul 01.
Article in English | MEDLINE | ID: mdl-37150366

ABSTRACT

The Inulinase from Kluyveromyces marxianus ISO3 (Inu-ISO3) is an enzyme able to hydrolyze linear fructans such as chicory inulin as well as branched fructans like agavin. This enzyme was cloned and expressed in Komagataella pastoris to study the role of selected aromatic and polar residues in the catalytic pocket by Alanine scanning. Molecular dynamics (MD) simulations and enzyme kinetics analysis were performed to study the functional consequences of these amino acid substitutions. Site-directed mutagenesis was used to construct the mutants of the enzyme after carrying out the MD simulations between Inu-ISO3 and its substrates. Mutation Trp79:Ala resulted in the total loss of activity when fructans were used as substrates, while with sucrose, the activity decreased by 98 %. In contrast, the mutations Phe113:Ala and Gln236:Ala increased the invertase activity when sucrose was used as a substrate. Although these amino acids are not part of the conserved motifs where the catalytic triad is located, they are essential for the enzyme's activity. In silico and experimental approaches corroborate the relevance of these residues for substrate binding and their influence on enzymatic activity.


Subject(s)
Kluyveromyces , Molecular Dynamics Simulation , Glycoside Hydrolases/chemistry , Kluyveromyces/genetics , Fructans/metabolism , Amino Acids/metabolism , Sucrose/metabolism
6.
Appl Biochem Biotechnol ; 195(3): 2028-2056, 2023 Mar.
Article in English | MEDLINE | ID: mdl-36401066

ABSTRACT

This work reports the characterization of an amylolytic enzyme from the bacteria Massilia timonae CTI-57. A gene encoding this protein was expressed from the pTrcHis2B plasmid in Escherichia coli BL21 Star™ (DE3). The purified protein had 64 kDa, and its modeled structure showed a monomer with the conserved α-amylases structure composed of the domain A with the characteristic (ß/α)8-barrel, the small domain B, and the domain C with an antiparallel beta-sheet. Phylogenetic analysis demonstrated that the expressed protein belongs to the GH13_19 subfamily of glycoside hydrolases. The ions Ca2+, Mn2+, Na+, Mg2+, Mo6+, and K+ did activate the purified enzyme, while EDTA and the ions Fe2+, Hg2+, Zn2+, and Cu2+ were strong inhibitors. SDS was also a strong inhibitor. The enzyme's optimal pH and temperature were 7.0 and 45 °C, respectively, and its Tm was 62.2 °C. The KM of the purified enzyme for starch was 13 mg/mL, and the Vmax was 0.24 µmol of reducing sugars released per min. The characterized enzyme presented higher specificity for maltodextrin and starch and produced maltose as the main starch hydrolysis product. This is the first characterized maltose-forming amylolytic enzyme from the GH13_19 subfamily. The purified enzyme produced ß-cyclodextrin from starch and maltodextrin and could be considered a cyclodextrin glucanotransferase (CGTase). This is the first report of a GH13_19 subfamily enzyme with CGTase activity.


Subject(s)
Glycoside Hydrolases , Maltose , Phylogeny , Glycoside Hydrolases/chemistry , alpha-Amylases/chemistry , Starch/metabolism , Bacteria/metabolism , Substrate Specificity
7.
Nat Chem Biol ; 19(2): 218-229, 2023 02.
Article in English | MEDLINE | ID: mdl-36443572

ABSTRACT

Bifidobacteria are early colonizers of the human gut and play central roles in human health and metabolism. To thrive in this competitive niche, these bacteria evolved the capacity to use complex carbohydrates, including mammalian N-glycans. Herein, we elucidated pivotal biochemical steps involved in high-mannose N-glycan utilization by Bifidobacterium longum. After N-glycan release by an endo-ß-N-acetylglucosaminidase, the mannosyl arms are trimmed by the cooperative action of three functionally distinct glycoside hydrolase 38 (GH38) α-mannosidases and a specific GH125 α-1,6-mannosidase. High-resolution cryo-electron microscopy structures revealed that bifidobacterial GH38 α-mannosidases form homotetramers, with the N-terminal jelly roll domain contributing to substrate selectivity. Additionally, an α-glucosidase enables the processing of monoglucosylated N-glycans. Notably, the main degradation product, mannose, is isomerized into fructose before phosphorylation, an unconventional metabolic route connecting it to the bifid shunt pathway. These findings shed light on key molecular mechanisms used by bifidobacteria to use high-mannose N-glycans, a perennial carbon and energy source in the intestinal lumen.


Subject(s)
Bifidobacterium longum , Mannose , Animals , Humans , Mannose/metabolism , Bifidobacterium longum/metabolism , Cryoelectron Microscopy , Polysaccharides/chemistry , Mannosidases/metabolism , Glycoside Hydrolases/chemistry , Bifidobacterium/metabolism , Mammals
8.
Acta Crystallogr D Struct Biol ; 78(Pt 11): 1358-1372, 2022 Nov 01.
Article in English | MEDLINE | ID: mdl-36322419

ABSTRACT

Glycoside hydrolase family 5 (GH5) harbors diverse substrate specificities and modes of action, exhibiting notable molecular adaptations to cope with the stereochemical complexity imposed by glycosides and carbohydrates such as cellulose, xyloglucan, mixed-linkage ß-glucan, laminarin, (hetero)xylan, (hetero)mannan, galactan, chitosan, N-glycan, rutin and hesperidin. GH5 has been divided into subfamilies, many with higher functional specificity, several of which have not been characterized to date and some that have yet to be discovered with the exploration of sequence/taxonomic diversity. In this work, the current GH5 subfamily inventory is expanded with the discovery of the GH5_57 subfamily by describing an endo-ß-mannanase (CapGH5_57) from an uncultured Bacteroidales bacterium recovered from the capybara gut microbiota. Biochemical characterization showed that CapGH5_57 is active on glucomannan, releasing oligosaccharides with a degree of polymerization from 2 to 6, indicating it to be an endo-ß-mannanase. The crystal structure, which was solved using single-wavelength anomalous diffraction, revealed a massively redesigned catalytic interface compared with GH5 mannanases. The typical aromatic platforms and the characteristic α-helix-containing ß6-α6 loop in the positive-subsite region of GH5_7 mannanases are absent in CapGH5_57, generating a large and open catalytic interface that might favor the binding of branched substrates. Supporting this, CapGH5_57 contains a tryptophan residue adjacent and perpendicular to the cleavage site, indicative of an anchoring site for a substrate with a substitution at the -1 glycosyl moiety. Taken together, these results suggest that despite presenting endo activity on glucomannan, CapGH5_57 may have a new type of substituted heteromannan as its natural substrate. This work demonstrates the still great potential for discoveries regarding the mechanistic and functional diversity of this large and polyspecific GH family by unveiling a novel catalytic interface sculpted to recognize complex heteromannans, which led to the establishment of the GH5_57 subfamily.


Subject(s)
Glycoside Hydrolases , beta-Mannosidase , Glycoside Hydrolases/chemistry , beta-Mannosidase/chemistry , beta-Mannosidase/metabolism , Mannans/chemistry , Mannans/metabolism , Substrate Specificity , Catalysis
9.
Molecules ; 26(21)2021 Oct 30.
Article in English | MEDLINE | ID: mdl-34770995

ABSTRACT

The proteins within the CAZy glycoside hydrolase family GH13 catalyze the hydrolysis of polysaccharides such as glycogen and starch. Many of these enzymes also perform transglycosylation in various degrees, ranging from secondary to predominant reactions. Identifying structural determinants associated with GH13 family reaction specificity is key to modifying and designing enzymes with increased specificity towards individual reactions for further applications in industrial, chemical, or biomedical fields. This work proposes a computational approach for decoding the determinant structural composition defining the reaction specificity. This method is based on the conservation of coevolving residues in spatial contacts associated with reaction specificity. To evaluate the algorithm, mutants of α-amylase (TmAmyA) and glucanotransferase (TmGTase) from Thermotoga maritima were constructed to modify the reaction specificity. The K98P/D99A/H222Q variant from TmAmyA doubled the transglycosydation/hydrolysis (T/H) ratio while the M279N variant from TmGTase increased the hydrolysis/transglycosidation ratio five-fold. Molecular dynamic simulations of the variants indicated changes in flexibility that can account for the modified T/H ratio. An essential contribution of the presented computational approach is its capacity to identify residues outside of the active center that affect the reaction specificity.


Subject(s)
Glycoside Hydrolases/metabolism , Algorithms , Glycoside Hydrolases/chemistry , Glycoside Hydrolases/genetics , Glycosylation , Hydrolysis , Models, Molecular , Mutation , Polysaccharides/chemistry , Polysaccharides/metabolism
10.
Int J Mol Sci ; 22(19)2021 Sep 30.
Article in English | MEDLINE | ID: mdl-34638973

ABSTRACT

The search for promising biomolecules such as chitooligosaccharides (COS) has increased due to the need for healing products that act efficiently, avoiding complications resulting from exacerbated inflammation. Therefore, this study aimed to produce COS in two stages of hydrolysis using chitosanases derived from Bacillus toyonensis. Additionally, this study aimed to structurally characterize the COS via mass spectrometry, to analyze their biocompatibility in acute toxicity models in vivo, to evaluate their healing action in a cell migration model in vitro, to analyze the anti-inflammatory activity in in vivo models of xylol-induced ear edema and zymosan-induced air pouch, and to assess the wound repair action in vivo. The structural characterization process pointed out the presence of hexamers. The in vitro and in vivo biocompatibility of COS was reaffirmed. The COS stimulated the fibroblast migration. In the in vivo inflammatory assays, COS showed an antiedematogenic response and significant reductions in leukocyte migration, cytokine release, and protein exudate. The COS healing effect in vivo was confirmed by the significant wound reduction after seven days of the experiment. These results indicated that the presence of hexamers influences the COS biological properties, which have potential uses in the pharmaceutical field due to their healing and anti-inflammatory action.


Subject(s)
Anti-Inflammatory Agents/administration & dosage , Biocompatible Materials/administration & dosage , Chitosan/administration & dosage , Ear Diseases/drug therapy , Edema/drug therapy , Oligosaccharides/administration & dosage , Wound Healing/drug effects , 3T3 Cells , Animals , Anti-Inflammatory Agents/chemistry , Bacillus/enzymology , Biocompatible Materials/chemistry , Cell Movement/drug effects , Cell Survival/drug effects , Chitosan/chemistry , Cytokines/metabolism , Disease Models, Animal , Ear Diseases/chemically induced , Edema/chemically induced , Female , Fibroblasts/drug effects , Fibroblasts/metabolism , Glycoside Hydrolases/chemistry , Hydrolysis , Inflammation/drug therapy , Inflammation/metabolism , Leukocytes/drug effects , Leukocytes/metabolism , Male , Mice , Mice, Inbred BALB C , Oligosaccharides/chemistry
11.
Biotechnol Bioeng ; 118(10): 4052-4064, 2021 10.
Article in English | MEDLINE | ID: mdl-34232504

ABSTRACT

The heteropolysaccharide xylan is a valuable source of sustainable chemicals and materials from renewable biomass sources. A complete hydrolysis of this major hemicellulose component requires a diverse set of enzymes including endo-ß-1,4-xylanases, ß-xylosidases, acetylxylan esterases, α-l-arabinofuranosidases, and α-glucuronidases. Notably, the most studied xylanases from glycoside hydrolase family 11 (GH11) have exclusively been endo-ß-1,4- and ß-1,3-xylanases. However, a recent analysis of a metatranscriptome library from a microbial lignocellulose community revealed GH11 enzymes capable of releasing solely xylobiose from xylan. Although initial biochemical studies clearly indicated their xylobiohydrolase mode of action, the structural features that drive this new activity still remained unclear. It was also not clear whether the enzymes acted on the reducing or nonreducing end of the substrate. Here, we solved the crystal structure of MetXyn11 in the apo and xylobiose-bound forms. The structure of MetXyn11 revealed the molecular features that explain the observed pattern on xylooligosaccharides released by this nonreducing end xylobiohydrolase.


Subject(s)
Composting , Disaccharides/chemistry , Glycoside Hydrolases/chemistry , Lignin/chemistry , Microbiota/genetics , Xylans/chemistry , Glycoside Hydrolases/genetics
12.
Int J Biol Macromol ; 186: 909-918, 2021 Sep 01.
Article in English | MEDLINE | ID: mdl-34274400

ABSTRACT

A purified exo-polygalacturonase of Neosartorya glabra (EplNg) was successfully characterized. EplNg native presented 68.2 kDa, with 32% carbohydrate content. The deglycosylated form showed 46.3 kDa and isoelectric point of 5.4. The identity of EplNg was confirmed as an exo-polygalacturonase class I (EC 3.2.1.67) using mass spectrometry and Western-Blotting. Capillary electrophoresis indicated that only galacturonic acid was released by the action of EplNg on sodium polypectate, confirming an exoenzyme character. The structural model confers that EplNg has a core formed by twisted parallel ß-sheets structure. Among twelve putative cysteines, ten were predicted to form disulfide bridges. The catalytic triad predicted is composed of Asp223, Asp245, and Asp246 aligned along with a distance in 4-5 Å, suggesting that EplNg probably does not perform the standard inverting catalytic mechanism described for the GH28 family. EplNg was active from 30 to 90 °C, with maximum activity at 65 °C, pH 5.0. The Km and Vmax determined using sodium polypectate were 6.9 mg·mL-1 and Vmax 690 µmol·min-1.mg-1, respectively. EplNg was active and stable over a wide range of pH values and temperatures, confirming the interesting properties EplNg and provide a basis for the development of the enzyme in different biotechnological processes.


Subject(s)
Aspergillus/enzymology , Fungal Proteins/metabolism , Glycoside Hydrolases/metabolism , Catalysis , Enzyme Stability , Fungal Proteins/chemistry , Fungal Proteins/isolation & purification , Glycoside Hydrolases/chemistry , Glycoside Hydrolases/isolation & purification , Hexuronic Acids/metabolism , Hydrogen-Ion Concentration , Kinetics , Models, Molecular , Pectins/metabolism , Protein Conformation , Protein Stability , Structure-Activity Relationship , Substrate Specificity , Temperature
13.
Nat Commun ; 12(1): 367, 2021 01 14.
Article in English | MEDLINE | ID: mdl-33446650

ABSTRACT

Xylanolytic enzymes from glycoside hydrolase family 43 (GH43) are involved in the breakdown of hemicellulose, the second most abundant carbohydrate in plants. Here, we kinetically and mechanistically describe the non-reducing-end xylose-releasing exo-oligoxylanase activity and report the crystal structure of a native GH43 Michaelis complex with its substrate prior to hydrolysis. Two distinct calcium-stabilized conformations of the active site xylosyl unit are found, suggesting two alternative catalytic routes. These results are confirmed by QM/MM simulations that unveil the complete hydrolysis mechanism and identify two possible reaction pathways, involving different transition state conformations for the cleavage of xylooligosaccharides. Such catalytic conformational promiscuity in glycosidases is related to the open architecture of the active site and thus might be extended to other exo-acting enzymes. These findings expand the current general model of catalytic mechanism of glycosidases, a main reaction in nature, and impact on our understanding about their interaction with substrates and inhibitors.


Subject(s)
Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Glycoside Hydrolases/chemistry , Glycoside Hydrolases/metabolism , Xanthomonas/enzymology , Bacterial Proteins/genetics , Binding Sites , Catalysis , Catalytic Domain , Crystallography, X-Ray , Glycoside Hydrolases/genetics , Kinetics , Models, Molecular , Oligosaccharides/chemistry , Oligosaccharides/metabolism , Xanthomonas/chemistry , Xanthomonas/genetics , Xylose/chemistry , Xylose/metabolism
14.
Molecules ; 26(2)2021 Jan 16.
Article in English | MEDLINE | ID: mdl-33467076

ABSTRACT

Cross-linked enzyme aggregates (CLEAs) of the Y509E mutant of glycoside hydrolase family 52 ß-xylosidase from Geobacillus stearothermophilus with dual activity of ß-xylosidase and xylanase (XynB2Y509E) were prepared. Ammonium sulfate was used as the precipitant agent, and glutaraldehyde as cross-linking agent. The optimum conditions were found to be 90% ammonium sulfate, 12.5 mM glutaraldehyde, 3 h of cross-linking reaction at 25 °C, and pH 8.5. Under these (most effective) conditions, XynB2Y509E-CLEAs retained 92.3% of their original ß-xylosidase activity. Biochemical characterization of both crude and immobilized enzymes demonstrated that the maximum pH and temperature after immobilization remained unchanged (pH 6.5 and 65 °C). Moreover, an improvement in pH stability and thermostability was also found after immobilization. Analysis of kinetic parameters shows that the K m value of XynB2Y509E-CLEAs obtained was slightly higher than that of free XynB2Y509E (1.2 versus 0.9 mM). Interestingly, the xylanase activity developed by the mutation was also conserved after the immobilization process.


Subject(s)
Amino Acid Substitution , Bacterial Proteins/chemistry , Cross-Linking Reagents/chemistry , Geobacillus stearothermophilus/enzymology , Glutaral/chemistry , Glycoside Hydrolases/chemistry , Protein Aggregates , Bacterial Proteins/genetics , Geobacillus stearothermophilus/genetics , Glycoside Hydrolases/genetics , Mutation, Missense
15.
Int J Biol Macromol ; 165(Pt A): 1482-1495, 2020 Dec 15.
Article in English | MEDLINE | ID: mdl-33017605

ABSTRACT

A chitosanase (CvCsn46) from Chromobacterium violaceum ATCC 12472 was produced in Escherichia coli, purified, and partially characterized. When subjected to denaturing polyacrylamide gel electrophoresis, the enzyme migrated as two protein bands (38 and 36 kDa apparent molecular masses), which were both identified as CvCsn46 by mass spectrometry. The enzyme hydrolyzed colloidal chitosan, with optimum catalytic activity at 50 °C, and two optimum pH values (at pH 6.0 and pH 11.0). The chitosanolytic activity of CvCsn46 was enhanced by some ions (Ca2+, Co2+, Cu2+, Sr2+, Mn2+) and DTT, whereas Fe2+, SDS and ß-mercaptoethanol completely inhibited its activity. CvCsn46 showed a non-Michaelis-Menten kinetics, characterized by a sigmoidal velocity curve (R2 = 0.9927) and a Hill coefficient of 3.95. ESI-MS analysis revealed that the hydrolytic action of CvCsn46 on colloidal chitosan generated a mixture of low molecular mass chitooligosaccharides, containing from 2 to 7 hexose residues, as well as D-glucosamine. The chitosan oligomers generated by CvCsn46 inhibited in vitro the mycelial growth of Lasiodiplodia theobromae, significantly reducing mycelium extension and inducing hyphal morphological alterations, as observed by scanning electron microscopy. CvCsn46 was characterized as a versatile biocatalyst that produces well-defined chitooligosaccharides, which have potential to control fungi that cause important crop diseases.


Subject(s)
Antifungal Agents/chemistry , Chitin/analogs & derivatives , Chromobacterium/genetics , Glycoside Hydrolases/genetics , Amino Acid Sequence/genetics , Chitin/biosynthesis , Chitin/chemistry , Chitin/genetics , Chitosan/chemistry , Chromobacterium/enzymology , Escherichia coli/genetics , Glycoside Hydrolases/biosynthesis , Glycoside Hydrolases/chemistry , Hydrogen-Ion Concentration , Hydrolysis , Molecular Weight , Oligosaccharides
16.
Biochim Biophys Acta Proteins Proteom ; 1868(12): 140533, 2020 12.
Article in English | MEDLINE | ID: mdl-32866628

ABSTRACT

The fungus Thermothielavioides terrestris plays an important role in the global carbon cycle with enzymes capable of degrading polysaccharides from biomass, therefore an attractive source of proteins to be investigated and understood. From cloning to a three-dimensional structure, we foster a deeper characterization of an α-ʟ-arabinofuranosidase, a glycoside hydrolase from the family 62 (TtAbf62), responsible to release arabinofuranose from non-reducing ends of polysaccharides. TtAbf62 was tested with synthetic (pNP-Araf) and polymeric substrates (arabinan and arabinoxylan), showing optimal temperature and pH (for pNP-Araf) of 30 °C and 4.5-5.0, respectively. Kinetic parameters revealed different specific activity for the three substrates, with a higher affinity for pNP-Araf (KM: 4 ± 1 mM). The hydrolyzing activity of TtAbf62 on sugarcane bagasse suggests high efficiency in the decomposition of arabinoxylan, abundant hemicellulose presented in the sugarcane cell wall. The crystal packing of TtAbf62 reveals an exquisite domain swapping, located at the supramolecular arrangement through a disulfide bond. All crystallographic behaviors go against its monomeric state in solution, indicating a crystal-induced artifact. Structural information will form the basis for further studies aiming the development of optimized enzymatic properties to be used in biotechnological applications.


Subject(s)
Ascomycota/enzymology , Glycoside Hydrolases/chemistry , Models, Molecular , Protein Conformation , Protein Interaction Domains and Motifs , Biochemical Phenomena , Catalysis , Glycoside Hydrolases/metabolism , Kinetics , Protein Binding , Recombinant Proteins , Spectrum Analysis , Structure-Activity Relationship
17.
Protein Expr Purif ; 176: 105718, 2020 12.
Article in English | MEDLINE | ID: mdl-32777449

ABSTRACT

Exo-inulinases are versatile enzymes that have gained attention in recent years due to their ability to hydrolyze linear and branched polyfructose chains found in inulines. Agavin, a branched inulin, is found in Agave plant, the raw matter to produce tequila. Our group has isolated several microbial strains from agave bagasse, an agro-industrial residue from tequila production that increases yearly. Strain ISO3, identified as Kluyveromyces marxianus, showed a remarkable activity towards agavin, and from its fermentation liquor an inulinolytic enzyme (Inu-ISO3) was purified. The isolated enzyme is a glycosylated dimeric protein with a molecular mass of ~256 kDa, as determined by DLS and SEC. The enzyme has an isoelectric pH of 4.6 and has both inulinase and invertase activities with an I/S ratio (ratio of activity with agavin to activity with sucrose) of 1.39. The enzyme has temperature and pH optima of 50 °C and 5.5, respectively, and follows hyperbolic kinetics with agavin (kcat of 339 ± 27 s-1 and KM of 11.8 ± 1.5 mM). The remarkable activity of Inu-ISO3 on linear and branched inulin spotlights this enzyme as a potential player in the treatment of agricultural residua for the generation of added-value products.


Subject(s)
Agave/microbiology , Fungal Proteins , Glycoside Hydrolases , Inulin/chemistry , Kluyveromyces , Fungal Proteins/chemistry , Fungal Proteins/isolation & purification , Glycoside Hydrolases/chemistry , Glycoside Hydrolases/isolation & purification , Hydrolysis , Kluyveromyces/enzymology , Kluyveromyces/isolation & purification
18.
Protein Sci ; 29(9): 1879-1889, 2020 09.
Article in English | MEDLINE | ID: mdl-32597558

ABSTRACT

In this work, we investigated how activity and oligomeric state are related in a purified GH1 ß-glucosidase from Spodoptera frugiperda (Sfßgly). Gel filtration chromatography coupled to a multiple angle light scattering detector allowed separation of the homodimer and monomer states and determination of the dimer dissociation constant (KD ), which was in the micromolar range. Enzyme kinetic parameters showed that the dimer is on average 2.5-fold more active. Later, we evaluated the kinetics of homodimerization, scanning the changes in the Sfßgly intrinsic fluorescence over time when the dimer dissociates into the monomer after a large dilution. We described how the rate constant of monomerization (koff ) is affected by temperature, revealing the enthalpic and entropic contributions to the process. We also evaluated how the rate constant (kobs ) by which equilibrium is reached after dimer dilution behaves when varying the initial Sfßgly concentration. These data indicated that Sfßgly dimerizes through the conformational selection mechanism, in which the monomer undergoes a conformational exchange and then binds to a similar monomer, forming a more active homodimer. Finally, we noted that conformational selection reports and experiments usually rely on a ligand whose concentration is in excess, but for homodimerization, this approach does not hold. Hence, since our approach overcomes this limitation, this study not only is a new contribution to the comprehension of GH1 ß-glucosidases, but it can also help to elucidate protein interaction pathways.


Subject(s)
Glycoside Hydrolases/chemistry , Insect Proteins/chemistry , Protein Multimerization , Spodoptera/enzymology , Animals , Glycoside Hydrolases/genetics , Insect Proteins/genetics , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Spodoptera/genetics
19.
Nat Chem Biol ; 16(8): 920-929, 2020 08.
Article in English | MEDLINE | ID: mdl-32451508

ABSTRACT

The fundamental and assorted roles of ß-1,3-glucans in nature are underpinned on diverse chemistry and molecular structures, demanding sophisticated and intricate enzymatic systems for their processing. In this work, the selectivity and modes of action of a glycoside hydrolase family active on ß-1,3-glucans were systematically investigated combining sequence similarity network, phylogeny, X-ray crystallography, enzyme kinetics, mutagenesis and molecular dynamics. This family exhibits a minimalist and versatile (α/ß)-barrel scaffold, which can harbor distinguishing exo or endo modes of action, including an ancillary-binding site for the anchoring of triple-helical ß-1,3-glucans. The substrate binding occurs via a hydrophobic knuckle complementary to the canonical curved conformation of ß-1,3-glucans or through a substrate conformational change imposed by the active-site topology of some fungal enzymes. Together, these findings expand our understanding of the enzymatic arsenal of bacteria and fungi for the breakdown and modification of ß-1,3-glucans, which can be exploited for biotechnological applications.


Subject(s)
Glucan 1,3-beta-Glucosidase/chemistry , Glycoside Hydrolases/chemistry , beta-Glucans/chemistry , Amino Acid Sequence/genetics , Binding Sites/physiology , Catalytic Domain/physiology , Crystallography, X-Ray/methods , Glucan 1,3-beta-Glucosidase/metabolism , Glucans/chemistry , Glycosides/chemistry , Models, Molecular , Substrate Specificity/physiology
20.
Int J Biol Macromol ; 154: 1082-1090, 2020 Jul 01.
Article in English | MEDLINE | ID: mdl-32151717

ABSTRACT

Glycosidases are enzymes involved in the cascade reactions leading to the release of aromatic compounds in white wines. However, the use of commercial soluble glycosidases is facing difficulties due to their fast inactivation, poor reaction control, low efficiency of enzyme use, and the presence of catalyst residues in the product. Co-immobilization as cross-linked enzyme aggregates (combi-CLEAs) is a sound alternative allowing the immobilization of enzymes in their own protein matrix, yielding highly stable and active biocatalysts. Notwithstanding, their micrometer sized particles limit their application in industrial processes. To overcome this, combi-CLEAs of ß-D-glucosidase (ßG) and α-L-arabinofuranosidase (ARA) were entrapped in polymeric chitosan beads. The effect of crosslinking reagents and crosslinking time on the specific activity and stability of combi-CLEAs was studied, and the best conditions for the entrapment of the combi-CLEAs in polymeric chitosan beads were determined varying the concentration of the chitosan solution and the pH of the gelation agent solution. The resulting biocatalyst beads (average diameter 1.24 mm), retained full activity after 91 days of incubation under winemaking conditions, having specific activities of 0.91 and 0.88 international units of activity per gram for ßG and ARA, respectively. Such characteristics make them suitable for aroma enhancement in wines.


Subject(s)
Chitosan/chemistry , Enzymes, Immobilized/chemistry , Glucosidases/chemistry , Glycoside Hydrolases/chemistry , Odorants , Wine , Cross-Linking Reagents , Enzyme Stability
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