GH57 amylopullulanase from Desulfurococcus amylolyticus JCM 9188 can make highly branched cyclodextrin via its transglycosylation activity

The crystal structure of GH57 family amylopullulanase reveals its dual binding pockets sharing the same catalytic dyad

Glycoside Hydrolase Family 57 (GH57) amylopullulanase is a thermophilic endoamylase capable of hydrolyzing both α-1,4 and α-1,6-glycosidic bonds, demonstrating significant potential for one-step starch saccharification in industrial applications. However, the mechanisms underlying the dual catalytic activities of GH57 family amylopullulanase remain poorly understood. In this study, we report the first crystal structures of a GH57 amylopullulanase from Aquifex aeolicus (AaApu) in complex with oligosaccharides containing both α-1,4 and α-1,6 glycosidic bonds. Our structural analysis reveals that GH57 amylopullulanase features dual binding pockets arranged in a "Y"-shaped configuration, which accommodates branched-chain starches. The dual binding pockets share a common catalytic dyad composed of Glu256 and Asp352. Notably, unlike the typical retaining mechanism observed in many glycoside hydrolases, the distance between the catalytic residues in GH57 amylopullulanase is significantly larger (approximately 7 Å). This study provides critical insights into the structural basis of GH57 amylopullulanase activity and offers a foundation for the rational engineering of these enzymes for industrial applications.

Dividing the α-amylase family GH57 of starch hydrolases and related enzymes into subfamilies using evolutionary, clustering and functional criteria

In the CAZy classification, four glycoside hydrolase families - GH13, GH57, GH119 and GH126 - have been designated as α-amylase families. The present study applied to a dataset of over 5000 family GH57 sequences, delivers a functionally balanced subdivision of the family GH57 into ten subfamilies. Eight of these subfamilies bear a specific enzyme activity: GH57_1, 4-α-glucanotransferases; GH57_2, amylopullulanases; GH57_3, α-amylases; GH57_4, α-galactosidases; GH57_5, α-glucan-branching enzymes; GH57_6, non-specified amylases; GH57_7, amylopullulanases-cyclomaltodextrinases; and GH57_8, maltogenic amylases. Two subfamilies, GH57_9 and GH57_10, not including any characterized members so far despite their conserved catalytic machinery, will deserve the community attention. Each subfamily is highlighted by its sequence fingerprints, through the logo of the five GH57 conserved sequence regions. The structural features are also compared with regard to domains complementing the catalytic module composed by the (β/α)7-barrel and the succeeding α-helical bundle. Characterized members in each subfamily display a strong agreement in their functional profile, indicating that the here proposed GH57 subfamily annotation results in functionally meaningful subsets. Moreover, several small groups of sequences still lacking sufficient sequence diversity and biochemical characterization did not integrate any of the created GH57 subfamilies so far; nevertheless, they could complete the overall GH57 subfamily picture in future.

Mechanistic insights into cyclodextrins as substrates and inhibitors of GH57 family amylopullulanase from Aquifex aeolicus

Maltooligosaccharides (MOs) have gained significant attention in the food and pharmaceutical industries owing to their valuable functional properties, including controlled sweetness, digestibility, and enhanced bioavailability. However, conventional MOs is production involves complex processing steps and significant production costs. A potential high-efficiency synthesis of specific MOs can be achieved through the ring-opening reaction of cyclodextrins (CDs) catalyzed by amylolytic enzymes. In this study, we analyze the catalytic conversion of α-, β-, and γ-CDs by a GH57 family amylopullulanase from Aquifex aeolicus (AaApu) using thin-layer chromatography (TLC). Our findings demonstrate that AaApu has a substrate specificity for γ-CD, while all three CDs exert competitive inhibition on pullulan hydrolysis. To elucidate the molecular mechanism of CDs as inhibitor and substrate of amylopullulanase, we determined high-resolution crystal structures of AaApu (wild-type and D352N) in complex with α-, β-, and γ-CD through co-crystallization. These findings establish a structure-function framework for understanding the bifunctional nature of CDs as both substrates and inhibitors in GH57 amylopullulanases.

Characterization of a maltononaose-producing amylopullulanase from Bacillus aryabhattai W310

The recombinated amylopullulanase of PulW310B, pullulanase from Bacillus aryabhattai W310, was characterized. Sequence analysis of PulW310B showed that PulW310B has type I pullulanase structures including its typical region and the conserved regions of glycoside hydrolase family 13. Moreover, PulW310B was predicted to has typical domains of pullulanase and SSF51445 belonging to tansglycosidase. While the substrate specificity of PulW310B presented that it is not a type I pullulanase. PulW310B could hydrolyze pullulan into maltotriose, maltohexaose, and maltononaose as main products with the proportions of 73.6 %, 16.7 %, and 6.7 %, which indicated that PulW310B has a certain potential on maltooligosaccharides production due to its 4-α-transglycosylation activity that was consistent with its domain analysis. Based on substrate specificity and hydrolytic properties, PulW310B is an amylopullulanase. This is the first report of maltononaose producing activity of amylopullulanase, which will be very useful in food industry. Moreover, PulW310B is a moderate pullulanase with optimal temperature of 40 °C and pH of 7.0. 50 % of the maximum activity was retained at room temperature (25 °C), which indicated that it is an environmentally friendly enzyme in maltooligosaccharides production.

Simultaneously improving the activity and thermostability of hyperthermophillic pullulanase by modifying the active-site tunnel and surface lysine

Pullulanases are important starch-debranching enzymes that mainly hydrolyze the α-1,6-glycosidic linkages in pullulan, starch, and oligosaccharides. Nevertheless, their practical applications are constrained because of their poor activity and low thermostability. Moreover, the trade-off between activity and thermostability makes it challenging to simultaneously improve them. In this study, an engineered pullulanase was developed through reshaping the active-site tunnel and engineering the surface lysine residues using the pullulanase from Pyrococcus yayanosii CH1 (PulPY2). The specific activity of the engineered pullulanase was increased 3.1-fold, and thermostability was enhanced 1.8-fold. Moreover, the engineered pullulanase exhibited 11.4-fold improvement in catalytic efficiency (kcat/Km). Molecular dynamics simulations demonstrated an anti-correlated movement around the entrance of active-site tunnel and stronger interactions between the surface residues in the engineered pullulanase, which would be beneficial to the activity and thermostability improvement, respectively. The strategies used in this study and dynamic evidence for insight into enzyme performance improvement may provide guidance for the activity and thermostability engineering of other enzymes.

Progress in cyclodextrins as important molecules regulating catalytic processes of glycoside hydrolases

Cyclodextrins (CDs) are important starch derivatives and commonly comprise α-, β-, and γ-CDs. Their hydrophilic surface and hydrophobic inner cavity enable regulation of enzyme catalysis through direct or indirect interactions. Clarifying interactions between CDs and enzyme is of great value for enzyme screening, mechanism exploration, regulation of catalysis, and applications. We summarize the interactions between CDs and glycoside hydrolases (GHs) according to two aspects: 1) CD as products, substrates, inhibitors and activators of enzymes, directly affecting the reaction process; 2) CDs indirectly affecting the enzymatic reaction by solubilizing substrates, relieving substrate/product inhibition, increasing recombinant enzyme production and storage stability, isolating and purifying enzymes, and serving as ligands in crystal structure to identify functional amino acid residues. Additionally, CD enzyme mimetics are developed and used as catalysts in traditional artificial enzymes as well as nanozymes, making the application of CDs no longer limited to GHs. This review concerns the regulation of GHs catalysis by CDs, and gives insights into research on interactions between enzymes and ligands.

Isolation, characterization, and cloning of thermostable pullulanase from Geobacillus stearothermophilus ADM-11

This study aimed to identify thermo-stable pullulanase-producing bacteria in soil samples of potato fields and food-producing companies. Pullulan agar medium was used to screen 17 bacterial strains, which were incubated at 65 °C. The isolate with the maximum activity (375U/ml) was selected and recognized as Geobacillus stearothermophilus ADM-11 by morphological, biochemical characterization, and 16S rRNA gene sequencing. The pullulanase production required optimum pH of 7 and temperature of 75 °C, respectively. The electrophoresis of purified pullulanase on SDS-polyacrylamide gel revealed 83 kDa of a molecular weight that is active at 70 °C and pH 7.0. It was also stable at 90 °C but its activity was decreased by 10 % at 100 °C. The action of pullulanase was increased and stabilized by Ca+2 among the metal ions. Beta and gamma-cyclodextrins inhibited enzyme activity while ethylenediaminetetraacetate (EDTA) and phenylmethylsulfonyl fluoride (PMSF) have no significant effect on pullulanase activity. A full-length pullulanase gene was amplified from G. stearothermophilus ADM-11 using genomic DNA 2.1 kb of PCR product which was then purified and ligated in the cloning vector pTZ57R using the TA cloning technique. Colony PCR confirmed cloning on the positive clones after the pullulanase gene had been ligated and subjected to restriction digestion. It revealed 74 % similarity with the reported pullulanase gene from Geobacillus sp. 44C. The thermostability of pullulanase and its ability to degrade raw pullulan may therefore have wide-scale applications in starch processing, the detergent business, and new biotechnological applications.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018

This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.

Characterization of a novel detergent-resistant type I pullulanase from Bacillus megaterium Y103 and its application in laundry detergent

This study aims to find a moderate pullulanase for detergent industry. The pulY103B gene (2217 bp) from Bacillus megaterium Y103 was cloned and expressed in Escherichia coli. PulY103B contained four conserved regions of glycoside hydrolase family (GH) 13 and the typical sequence of type I pullulanase. The optimal reaction conditions of PulY103B were pH 6.5 and 40 °C. In addition, it remained stable below 40 °C and over 80% of activity was retained at pH ranging from 6.0 to 8.5. The best substrate for the enzyme was pullulan. Furthermore, it exhibited activity toward wheat starch (36.5%) and soluble starch (33.4%) but had no activity toward amylose and glycogen. Maltotriose and maltohexaose were major pullulan hydrolysis products. Soluble starch and amylopectin were mainly hydrolyzed into maltotetraose. These results indicated that PulY103B is a novel type I pullulanase with transglycosylation activity via formation of α-1,4-glucosidic linkages. Moreover, PulY103B was strongly stimulated by nonionic detergents [viz, Tween 20 (10%), Tween 80 (1%), Triton X-100 (20%)] and commercial liquid detergents (3.0 g/L). Wash performance tests demonstrated that the mixture of PulY103B and detergent removed starch-based stains better than using detergent alone (p < 0.05). Therefore, this pullulanase has big potential as a detergent additive.

Modulating the pH profile of the pullulanase from Pyrococcus yayanosii CH1 by synergistically engineering the active center and surface

A preferable pullulanase with high thermostability and catalytic activity at pH 4.5-5 is desired to match with glucoamylase in the starch-saccharification process. However, most of them exhibit low activity under such low pH conditions. Here, the optimal pH of the hyperthermostable pullulanase from Pyrococcus yayanosii (Pul_PY2) was successfully shifted from 6.4 to 5 with a 2-fold increase in the specific activity based on synergistic engineering of the active center and surface. Synergistic engineering was performed by introducing histidine within 6 Å of the active sites, and by enhancing negative charges on the enzymatic surface. Two single-site mutants of Pul_PY2-Q13H and Pul_PY2-I25E with higher hydrolytic activity were obtained, the optimal pH of which was shifted to pH 5 and 5.4, respectively; the combined mutant Pul_PY2-Q13H/I25E exhibited the optimal pH of 5, 3.2-fold increasing catalytic efficiency at pH 5, and high thermostability compared to Pul_PY2. These results not only obtained an applicable pullulanase for industrial application, but also provided a strategy for shifting the optimal pH of the enzyme based on synergistic engineering of the active center and surface.

Application of starch-based nanoparticles and cyclodextrin for prebiotics delivery and controlled glucose release in the human gut: a review

Starches are a major constituent of staple foods and are the main source of energy in the human diet (55-70%). In the gastrointestinal tract, starches are hydrolyzed into glucose by α-amylase and α-glucosidase, which leads to a postprandial glucose elevation. High levels of blood glucose levels over sustained periods may promote type 2 diabetes mellitus (T2DM) and obesity. Increasing consumption of starchy foods with a lower glycemic index may therefore contribute to improved health. In this paper, the preparation and properties of several starch-based nanoparticles (SNPs) and cyclodextrins (CDs) derivatives are reviewed. In particular, we focus on the various mechanisms responsible for the ability of these edible nanomaterials to modulate glucose release and the gut microbiome in the gastrointestinal tract. The probiotic functions are achieved through encapsulation and protection of prebiotics or bioactive components in foods or the human gut. This review therefore provides valuable information that could be used to design functional foods for improving human health and wellbeing.

Microbial starch debranching enzymes: Developments and applications

Starch debranching enzymes (SDBEs) hydrolyze the α-1,6 glycosidic bonds in polysaccharides such as starch, amylopectin, pullulan and glycogen. SDBEs are also important enzymes for the preparation of sugar syrup, resistant starch and cyclodextrin. As the synergistic catalysis of SDBEs and other starch-acting hydrolases can effectively improve the raw material utilization and production efficiency during starch processing steps such as saccharification and modification, they have attracted substantial research interest in the past decades. The substrate specificities of the two major members of SDBEs, pullulanases and isoamylases, are quite different. Pullulanases generally require at least two α-1,4 linked glucose units existing on both sugar chains linked by the α-1,6 bond, while isoamylases require at least three units of α-1,4 linked glucose. SDBEs mainly belong to glycoside hydrolase (GH) family 13 and 57. Except for GH57 type II pullulanse, GH13 pullulanases and isoamylases share plenty of similarities in sequence and structure of the core catalytic domains. However, the N-terminal domains, which might be one of the determinants contributing to the substrate binding of SDBEs, are distinct in different enzymes. In order to overcome the current defects of SDBEs in catalytic efficiency, thermostability and expression level, great efforts have been made to develop effective enzyme engineering and fermentation strategies. Herein, the diverse biochemical properties and distinct features in the sequence and structure of pullulanase and isoamylase from different sources are summarized. Up-to-date developments in the enzyme engineering, heterologous production and industrial applications of SDBEs is also reviewed. Finally, research perspective which could help understanding and broadening the applications of SDBEs are provided.

Industrially produced pullulanases with thermostability: Discovery, engineering, and heterologous expression

Pullulanases (EC 3.2.1.41) are well-known starch-debranching enzymes widely used to hydrolyze α-1,6-glucosidic linkages in starch, pullulan, amylopectin, and other oligosaccharides, with application potentials in food, brewing, and pharmaceutical industries. Although extensive studies are done to discover and express pullulanases, only few are available with desirable characteristics for industrial applications. This raises the challenge to mine new enzyme sources, engineer proteins based on sequence/structure, and regulate expressions. We review here the identification of extremophilic and mesophilic microbes as sources of industrial pullulanases with desirable characteristics, including acid-resistance, thermostability, and psychrotrophism. We present current advances in site-directed mutagenesis and sequence/structure-guided protein engineering of pullulanases. In addition, we discuss heterologous expression of pullulanases in prokaryotic and eukaryotic microbial systems, and address the effectiveness of the expression elements and their regulation of enzyme production. Finally, we indicate future research needs to develop desired industrial pullulanases.

In silico analysis of the α-amylase family GH57: eventual subfamilies reflecting enzyme specificities

Glycoside hydrolases (GHs) have been classified in the CAZy database into 153 GH families. Currently, there might be four α-amylase families: the main family GH13, the family GH57 with related GH119 and, eventually, also GH126. The family GH57 was established in 1996 as the second and smaller α-amylase family. In addition to α-amylase, it contains 4-α-glucanotransferase, α-glucan branching enzyme, amylopullulanase, dual-specificity amylopullulanase–cyclomaltodextrinase, non-specified amylase, maltogenic amylase and α-galactosidase. The family GH57 enzymes employ the retaining reaction mechanism, share five typical conserved sequence regions and possess catalytic (β/α)₇-barrel succeeded by a four-helix bundle with the catalytic machinery consisting of catalytic nucleophile and proton donor (glutamic acid and aspartic acid at strands β4 and β7, respectively). The present bioinformatics study delivers a detailed sequence comparison of 1602 family GH57 sequences with the aim to highlight the uniqueness of each enzyme’s specificity and all eventual protein groups. This was achieved by creating the evolutionary tree focused on both the enzyme specificities and taxonomical origin. The substantial increase of numbers of sequences from recent comparisons done more than 5 years ago has allowed to refine the details of the sequence logos for the individual enzyme specificities. The study identifies a new evolutionary distinct group of α-galactosidase-related enzymes with until-now-undefined enzyme specificity but positioned on the evolutionary tree on a branch adjacent to α-galactosidases. The specificity of α-galactosidase is, moreover, the only one of the entire family GH57 for which there is no structural support for the proposal of the proton donor based on sequence analysis. The analysis also suggests a few so-called “like” protein groups related to some family GH57 enzyme specificities but lacking one or both catalytic residues.