Structure and function of the type III pullulan hydrolase from Thermococcus kodakarensis

Pullulanase: unleashing the power of enzyme with a promising future in the food industry

Pullulanases are the most important industrial group of enzymes in family 13 glycosyl hydrolases. They hydrolyze either α-1,6 and α-1,4 or both glycosidic bonds in pullulan as well as other carbohydrates to produce glucose, maltose, and maltotriose syrups, which have important uses in food and other related sectors. However, very less reports are available on pullulanase production from native strains because of low yield issues. In line with the increasing demands for pullulanase, it has become important to search for novel pullulanase-producing microorganisms with high yields. Moreover, high production costs and low yield are major limitations in the industrial production of pullulanase enzymes. The production cost of pullulanase by using the solid-state fermentation (SSF) process can be minimized by selecting agro-industrial waste. This review summarizes the types, sources, production strategies, and potential applications of pullulanase in different food and other related industries. Researchers should focus on fungal strains producing pullulanase for better yield and low production costs by using agro-waste. It will prove a better enzyme in different food processing industries and will surely reduce the cost of products.

A Novel Subfamily GH13_46 of the α-Amylase Family GH13 Represented by the Cyclomaltodextrinase from Flavobacterium sp. No. 92

In the CAZy database, the α-amylase family GH13 has already been divided into 45 subfamilies, with additional subfamilies still emerging. The presented in silico study was undertaken in an effort to propose a novel GH13 subfamily represented by the experimentally characterized cyclomaltodxtrinase from Flavobacterium sp. No. 92. Although most cyclomaltodextrinases have been classified in the subfamily GH13_20. This one has not been assigned any GH13 subfamily as yet. It possesses a non-specified immunoglobulin-like domain at its N-terminus mimicking a starch-binding domain (SBD) and the segment MPDLN in its fifth conserved sequence region (CSR) typical, however, for the subfamily GH13_36. The searches through sequence databases resulted in collecting a group of 108 homologs forming a convincing cluster in the evolutionary tree, well separated from all remaining GH13 subfamilies. The members of the newly proposed subfamily share a few exclusive sequence features, such as the "aromatic" end of the CSR-II consisting of two well-conserved tyrosines with either glycine, serine, or proline in the middle or a glutamic acid succeeding the catalytic proton donor in the CSR-III. Concerning the domain N of the representative cyclomaltodextrinase, docking trials with α-, β- and γ-cyclodextrins have indicated it may represent a new type of SBD. This new GH13 subfamily has been assigned the number GH13_46.

Characterization of a novel thermostable phospholipase C from T. kodakarensis suitable for oil degumming

The implementation of cleaner technologies that minimize environmental pollution caused by conventional industrial processes is an increasing global trend. Hence, traditionally used chemicals have been replaced by novel enzymatic alternatives in a wide variety of industrial-scale processes. Enzymatic oil degumming, the first step of the oil refining process, exploits the conversion catalyzed by phospholipases to remove vegetable crude oils' phospholipids. This enzymatic method reduces the gums' volume and increases the overall oil yield. A thermostable phospholipase would be highly advantageous for industrial oil degumming as oil treatment at higher temperatures would save energy and increase the recovery of oil by facilitating the mixing and gums removal. A thermostable phosphatidylcholine (PC) (and phosphatidylethanolamine (PE))-specific phospholipase C from Thermococcus kodakarensis (TkPLC) was studied and completely removed PC and PE from crude soybean oil at 80 °C. Due to these characteristics, TkPLC is an interesting promising candidate for industrial-scale enzymatic oil degumming at high temperatures. KEY POINTS: • A thermostable phospholipase C from T. kodakarensis (TkPLC) has been identified. • TkPLC was recombinantly produced in Pichia pastoris and successfully purified. • TkPLC completely hydrolyzed PC and PE in soybean oil degumming assays at 80 °C.

A Bibliometric Analysis and Review of Pullulan-Degrading Enzymes—Past and Current Trends

Starch and pullulan degrading enzymes are essential industrial biocatalysts. Pullulan-degrading enzymes are grouped into pullulanases (types I and type II) and pullulan hydrolase (types I, II and III). Generally, these enzymes hydrolyse the α-1,6 glucosidic bonds (and α-1,4 for certain enzyme groups) of substrates and form reducing sugars such as glucose, maltose, maltotriose, panose or isopanose. This review covers two main aspects: (i) bibliometric analysis of publications and patents related to pullulan-degrading enzymes and (ii) biological aspects of free and immobilised pullulan-degrading enzymes and protein engineering. The collective data suggest that most publications involved researchers within the same institution or country in the past and current practice. Multi-national interaction shall be improved, especially in tapping the enzymes from unculturable prokaryotes. While the understanding of pullulanases may reach a certain extend of saturation, the discovery of pullulan hydrolases is still limited. In this report, we suggest readers consider using the next-generation sequencing technique to fill the gaps of finding more new sequences encoding pullulan-degrading enzymes to expand the knowledge body of this topic.

Structural basis of carbohydrate binding in domain C of a type I pullulanase fromPaenibacillus barengoltzii

Pullulanase (EC 3.2.1.41) is a well known starch-debranching enzyme that catalyzes the cleavage of α-1,6-glycosidic linkages in α-glucans such as starch and pullulan. Crystal structures of a type I pullulanase fromPaenibacillus barengoltzii(PbPulA) and ofPbPulA in complex with maltopentaose (G5), maltohexaose (G6)/α-cyclodextrin (α-CD) and β-cyclodextrin (β-CD) were determined in order to better understand substrate binding to this enzyme.PbPulA belongs to glycoside hydrolase (GH) family 13 subfamily 14 and is composed of three domains (CBM48, A and C). Three carbohydrate-binding sites identified inPbPulA were located in CBM48, near the active site and in domain C, respectively. The binding site in CBM48 was specific for β-CD, while that in domain C has not been reported for other pullulanases. The domain C binding site had higher affinity for α-CD than for G6; a small motif (FGGEH) seemed to be one of the major determinants for carbohydrate binding in this domain. Structure-based mutations of several surface-exposed aromatic residues in CBM48 and domain C had a debilitating effect on the activity of the enzyme. These results suggest that both CBM48 and domain C play a role in binding substrates. The crystal forms described contribute to the understanding of pullulanase domain–carbohydrate interactions.

Understanding Thermostability Factors of Barley Limit Dextrinase by Molecular Dynamics Simulations

Limit dextrinase (LD) is the only endogenous starch-debranching enzyme in barley (Hordeum vulgare, Hv), which is the key factor affecting the production of a high degree of fermentation. Free LD will lose its activity in the mashing process at high temperature in beer production. However, there remains a lack of understanding on the factor affecting the themostability of HvLD at the atomic level. In this work, the molecular dynamics simulations were carried out for HvLD to explore the key factors affecting the thermal stability of LD. The higher value of root mean square deviation (RMSD), radius of gyration (R_g), and surface accessibility (SASA) suggests the instability of HvLD at high temperatures. Intra-protein hydrogen bonds and hydrogen bonds between protein and water decrease at high temperature. Long-lived hydrogen bonds, salt bridges, and hydrophobic contacts are lost at high temperature. The salt bridge interaction analysis suggests that these salt bridges are important for the thermostability of HvLD, including E568–R875, D317–R378, D803–R884, D457–R214, D468–R395, D456–R452, D399–R471, and D541–R542. Root mean square fluctuation (RMSF) analysis identified the thermal-sensitive regions of HvLD, which will facilitate enzyme engineering of HvLD for enhanced themostability.

An overview of 25 years of research on Thermococcus kodakarensis, a genetically versatile model organism for archaeal research

Almost 25 years have passed since the discovery of a planktonic, heterotrophic, hyperthermophilic archaeon named Thermococcus kodakarensis KOD1, previously known as Pyrococcus sp. KOD1, by Imanaka and coworkers. T. kodakarensis is one of the most studied archaeon in terms of metabolic pathways, available genomic resources, established genetic engineering techniques, reporter constructs, in vitro transcription/translation machinery, and gene expression/gene knockout systems. In addition to all these, ease of growth using various carbon sources makes it a facile archaeal model organism. Here, in this review, an attempt is made to reflect what we have learnt from this hyperthermophilic archaeon.

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.

Advances and challenges in the production of extracellular thermoduric pullulanases by wild-type and recombinant microorganisms: a review

Thermoduric pullulanases, acting as starch-debranching enzymes, are required in many industrial applications, mainly in the production of concentrated glucose, maltose, and fructose syrups. To date, however, a single pullulanase, from Bacillus acidopullulyticus, is available on the market for industrial purposes. This review is an investigation of the major advances as well as the major challenges being faced with regard to optimization of the production of extracellular thermoduric pullulanases either by their original hosts or by recombinant organisms. The critical aspects linked to industrial pullulanase production, which should always be considered, are emphasized, including those parameters influencing solubility, thermostability, and catalytic efficiency of the enzyme. This review provides new insights for improving the production of extracellular thermoduric pullulanases in the hope that such information may facilitate their commercial utilization and potentially be applied to the development of other industrially relevant enzymes.

Structural features of a bacterial cyclic α-maltosyl-(1→6)-maltose (CMM) hydrolase critical for CMM recognition and hydrolysis

Cyclic α-maltosyl-(1→6)-maltose (CMM, cyclo-{→6)-α-d-Glcp-(1→4)-α-d-Glcp-(1→6)-α-d-Glcp-(1→4)-α-d-Glcp-(1→})is a cyclic glucotetrasaccharide with alternating α-1,4 and α-1,6 linkages. CMM is composed of two maltose units and is one of the smallest cyclic glucooligosaccharides. Although CMM is resistant to usual amylases, it is efficiently hydrolyzed by CMM hydrolase (CMMase), belonging to subfamily 20 of glycoside hydrolase family 13 (GH13_20). Here, we determined the ligand-free crystal structure of CMMase from the soil-associated bacterium Arthrobacter globiformis and its structures in complex with maltose, panose, and CMM to elucidate the structural basis of substrate recognition by CMMase. The structures disclosed that although the monomer structure consists of three domains commonly adopted by GH13 and other α-amylase-related enzymes, CMMase forms a unique wing-like dimer structure. The complex structure with CMM revealed four specific subsites, namely -3', -2, -1, and +1'. We also observed that the bound CMM molecule adopts a low-energy conformer compared with the X-ray structure of a single CMM crystal, also determined here. Comparison of the CMMase active site with those in other enzymes of the GH13_20 family revealed that three regions forming the wall of the cleft, denoted PYF (Pro-203/Tyr-204/Phe-205), CS (Cys-163/Ser-164), and Y (Tyr-168), are present only in CMMase and are involved in CMM recognition. Combinations of multiple substitutions in these regions markedly decreased the activity toward CMM, indicating that the specificity for this cyclic tetrasaccharide is supported by the entire shape of the pocket. In summary, our work uncovers the mechanistic basis for the highly specific interactions of CMMase with its substrate CMM.