Properties and active center of the thermostable branching enzyme from Bacillus stearothermophilus

Deciphering Biosynthesis Mechanism and Solution Properties of Cyclic Amylopectin

A novel cyclic amylopectin (CA) was synthesized from waxy corn starch (WCS) using Bacillus stearothermophilus branching enzyme (BstBE), providing insights into its biosynthesis mechanism and solution properties. During the first 4 h, BstBE partially cyclized WCS, producing 68.20% CA with a significantly reduced molecular weight (MW), from 8.98 × 10⁶ to 3.19 × 10⁴ g/mol and a lower polymer dispersity index (PDI), decreasing from 1.97 to 1.12. This resulted in a uniform CA structure with shorter chain lengths, particularly increasing DP 3-13, especially DP 7-9. Over the subsequent 4-12 h, the PDI slightly increased to 1.18 as the CA content decreased to 50.48%, with an increase in small ring structures (DP 6-12) of CA, suggesting both ring-opening and ring-downsizing due to continued enzyme catalysis. These results propose a two-stage reaction model: initial cyclization followed bybranching and secondary cyclization. CA exhibited excellent solution properties, with BE-4 and BE-12 samples demonstrating high solubility (≥65 g/100 mL), low viscosity (<0.01 Pa·s), and over 90% light transmittance after 14 days at 4 °C, highlighting its broad application potential.

Retrogradation inhibition and intragranular distribution in cooked rice by addition of α-glucosidase (AG) and branching enzyme (BE)

The effect of inhibiting retrogradation and changes in chain length distribution by AG and BE, which are texture-modifying enzymes, has been clarified. To ascertain in which part of the rice grain retrogradation occurs and which enzymes is most effective, the degree of retrogradation in each part of the rice grain was measured from the surface to the core of the same rice grain using a synchrotron radiation X-ray beam with a beam size of 100 μm. Retrogradation was effectively suppressed at all measurement sites by enzyme addition, although the effect of enzymes was greater at the surface. Rice grain sections were stained with iodine and eosin. A starch layer that does not easily form a complex with iodine was observed inside the protein layer at the surface of cooked rice. A starch layer with a long molecular chain that forms complexes with iodine was observed inside the rice grain.

Elucidation of the noncovalent interactions driving enzyme activity guides branching enzyme engineering for α-glucan modification

Branching enzymes (BEs) confer to α-glucans, the primary energy-storage reservoir in nature, a variety of features, like slow digestion. The full catalytic cycle of BEs can be divided in six steps, namely two covalent catalytic steps involving glycosylation and transglycosylation, and four noncatalytic steps involving substrate binding and transfers (SBTs). Despite the ever-growing wealth of biochemical and structural information on BEs, clear mechanistic insights into SBTs from an industrial-performance perspective are still missing. Here, we report a Rhodothermus profundi BE (RpBE) endowed with twice as much enzymatic activity as the Rhodothermus obamensis BE currently used in industry. Furthermore, we focus on the SBTs for RpBE by means of large-scale computations supported by experiment. Engineering of the crucial positions responsible for the initial substrate-binding step improves enzymatic activity significantly, while offering a possibility to customize product types. In addition, we show that the high-efficiency substrate-transfer steps preceding glycosylation and transglycosylation are the main reason for the remarkable enzymatic activity of RpBE, suggestive of engineering directions for the BE family.

Conserved residues Glu and Phe at substrate binding groove of α-1,6-glucanases modulate branch of the product

Understanding what amino acids in α-1,6-glucanases target α-1,6 glycosidic bonds of polysaccharides is timely and important for generating products with branch structure. With this objective, we investigated 330 sequences from seven subfamilies to excavate amino acids for recognition or catalysis of α-1,6 glycosidic bonds. Computational analysis identified two amino acids, E343 and W521, trigger α-1,6 glycosidic bond specificity of enzymes. To explore the effect of E343 and W521 on the product structure, several engineered mutants were studied in our research. Product structural analysis showed that the ratio of amylose and amylopectin is obviously different. The catalytic mechanism revealed that the bulky aromatic side chain is a trigger that controls the ratio of branch glucans. The E148 acts as a proton donor to regulate the generation of branched structures in the product during transglycosidation of the glucan branching enzyme (GBE).

Biochemical characteristics and potential application of a thermostable starch branching enzyme from Bacillus licheniformis

Slowly digestible starch (SDS) has attracted increasing attention for its function of preventing metabolic diseases. Based on transglycosylation, starch branching enzymes (1,4-α-glucan branching enzymes, GBEs, EC 2.4.1.18) can be used to regulate the digestibility of starch. In this study, a GBE gene from Bacillus licheniformis (bl-GBE) was cloned, expressed, purified, and characterized. Sequence analysis and structural modeling showed that bl-GBE belong to the glycoside hydrolase 13 (GH13) family, with which its active site residues were conserved. The bl-GBE was highly active at 80 °C and a pH range of 7.5-9.0, and retained 90% of enzyme activity at 70 °C for 16 h. bl-GBE also showed high substrate specificity (80.88 U/mg) on potato starch. The stability and the changes of the secondary structure of bl-GBE at different temperature were determined by circular dichroism (CD) spectroscopy. The CD data showed a loss of 20% of the enzyme activity at high temperatures (80 °C), due to the decreased content of the α -helix in the secondary structure. Furthermore, potato starch treated with bl-GBE (300 U/g starch) showed remarkable increase in stability, solubility, and significant reduction viscosity. Meanwhile, the slowly digestible starch content of bl-GBE modified potato starch increased by 53.03% compared with native potato starch. Our results demonstrated the potential applications of thermophilic bl-GBE in food industries.

Preparation of Slowly Digested Corn Starch Using Branching Enzyme and Immobilized α-Amylase

The aim of this study was to modify the digestibility and structure of corn starch by treatment with compound enzymes. Corn starch was treated with two enzymes (α-amylase, which catalyzes hydrolysis, and branching enzyme, a transglycosidase that catalyzes branch formation), and the reaction was monitored by determining the content of slowly digestible starch in the reaction product. The fine structure and physical and chemical properties of enzyme-modified starch samples were analyzed using scanning electron microscopy, gel chromatography, and X-ray diffraction methods; modified starch has a high degree of branching, a high proportion of short-chain branched structures, and greatly improved solubility. The results show that the slow digestion performance of corn starch was significantly improved after hydrolysis by α-amylase for 4 h and treatment with branching enzyme for 6 h. These results show that enzymatic modification of corn starch can improve its slow digestibility properties.

The Candida glabrata glycogen branching enzyme structure reveals unique features of branching enzymes of the Saccharomycetaceae phylum

Branching enzymes (BE) are responsible for the formation of branching points at the 1,6 position in glycogen and starch, by catalyzing the cleavage of α-1,4-linkages and the subsequent transfer by introducing α-1,6-linked glucose branched points. BEs are found in the large GH13 family, eukaryotic BEs being mainly classified in the GH13_8 subfamily, GH13_9 grouping almost exclusively prokaryotic enzymes. With the aim of contributing to the understanding of the mode of recognition and action of the enzymes belonging to GH13_8, and to the understanding of features distinguishing these enzymes from those belonging to subfamily 13_9 we solved the crystal structure of the glycogen branching enzyme (GBE) from the yeast Candida glabrata, CgGBE, in ligand free forms and in complex with a maltotriose. The structures revealed the presence of a domain already observed in Homo sapiens and Oryza sativa BEs and that we named α-helical N-terminal domain, in addition to the three conserved domains found in BE. We confirmed by phylogenetic analysis that this α-helical N-terminal domain is always present in the GH13_8 enzymes suggesting that it could actually present a signature for this subfamily. We identified two binding sites (BS) in the α-helical N-terminal domain and in the carbohydrate binding module 48 (CBM48), respectively, which show a unique structural organization only present in the Saccharomycotina phylum. Our structural and phylogenetic investigation provides new insight into the structural characterization of GH13_8 GBE revealing unique structural features only present in the Saccharomycotina phylum thereby conferring original properties to this group of enzymes.

Flexible Loop in Carbohydrate-Binding Module 48 Allosterically Modulates Substrate Binding of the 1,4-α-Glucan Branching Enzyme

The 1,4-α-glucan branching enzyme (GBE, EC 2.4.1.18) catalyzes the formation of α-1,6 branching points in starch and plays a key role in synthesis. To obtain mechanistic insights into the catalytic action of the enzyme, we first determined the crystal structure of GBE from Rhodothermus obamensis STB05 (RoGBE) to a resolution of 2.39 Å (PDB ID: 6JOY). The structure consists of three domains: domain A, domain C, and the carbohydrate-binding module 48 (CBM48). An engineered truncated mutant lacking the CBM48 domain (ΔCBM48) showed significantly reduced ligand binding affinity and enzyme activity. Comparison of the structures of RoGBE with other GBEs showed that CBM48 of RoGBE had a longer flexible loop. Truncation of the flexible loops resulted in reduced binding affinity and activity, thereby substantiating the importance of the optimum loop structure for catalysis. In essence, our study shows that CBM48, especially the flexible loop, plays an important role in substrate binding and enzymatic activity of RoGBE. Further, based on the structural analysis, kinetics, and activity assays on wild type and mutants, as well as homology modeling, we proposed a mechanistic model (called the "lid model") to illustrate how the flexible loop triggers substrate binding, ultimately leading to catalysis.

Expression and characterization of 1,4-α-glucan branching enzyme from Microvirga sp. MC18 and its application in the preparation of slowly digestible starch

Nutraceuticals containing modified starch with increased content of slowly-digestible starch (SDS) may reduce the prevalence of obesity, diabetes and cardiovascular diseases due to its slow digestion rate. Enzymatic methods for the preparation of modified starch have attracted increasing attention because of their low environmental impact, safety and specificity. In this study, the efficient glucan branching enzyme McGBE from Microvirga sp. MC18 was identified, and its relevant properties as well as its potential for industrial starch modification were evaluated. The purified McGBE exhibited the highest specificity for potato starch, with a maximal specific activity of 791.21 U/mg. A time-dependent increase in the content of α-1,6 linkages from 3.0 to 6.0% was observed in McGBE-modified potato starch. The proportion of shorter chains (degree of polymerization, DP < 13) increased from 29.2 to 63.29% after McGBE treatment, accompanied by a reduction of the medium length chains (DP 13-24) from 52.30 to 35.99% and longer chains (DP > 25) from 18.51 to 0.72%. The reduction of the storage modulus (G') and retrogradation enthalpy (ΔHr) of potato starch with increasing treatment time demonstrated that McGBE could inhibit the short- and long-term retrogradation of starch. Under the optimal conditions, the SDS content of McGBE-modified potato starch increased by 65.8% compared to native potato starch. These results suggest that McGBE has great application potential for the preparation of modified starch with higher SDS content that is resistant to retrogradation.

Enzymatic properties of an efficient glucan branching enzyme and its potential application in starch modification

Glucan branching enzymes (GBEs, EC 2.4.1.18) catalyze the formation of α-1,6-linked branch in starch, which is important for the starch modification with prospective properties. In this study, the aqGBE gene encoding an efficient glucan branching enzyme was cloned from Aquabacterium sp. strain A7-Y and successfully expressed in Escherichia coli BL21 (DE3). The specific activity of the purified recombinant enzyme rAqGBE was 2850 U/mg with potato starch as the optimal substrate, and the K_m and V_max values of rAqGBE were 1.18 mg/mL and 588.2 μmol/min/mg, respectively. Enzymological characterization showed that rAqGBE exhibits its optimal activity under the condition of 40 °C and pH 7.0, respectively, which is independent of calcium ions. Otherwise, rAqGBE-treated potato starch showed different chain length distribution compared with control, the numbers of short chains (degree of polymerization, DP < 7) and long chains (DP > 25) increased from 4.5% to 9.6% and 6.1%-15.7% after enzymatic treatment, respectively. In starch anti-ageing assay, with minimum usage of 0.8 mg rAqGBE per g starch, the rAqGBE-treated potato starch exhibited reduced retrogradation properties. Our results indicate that the branching enzyme AqGBE may therefore be a promising tool for the enzymatic modification of starch.

Recombinant expression and characterization of the glycogen branching enzyme from Vibrio vulnificus and its application in starch modification

Resistant starch (RS) is helpful in controlling and preventing metabolic syndrome relevant diseases. However, the RS content of natural starch and modified starch produced by enzymatic method is generally low. To solve this problem, we selected the glycogen branching enzyme from Vibrio vulnificus (VvGBE) and investigated its application. Firstly, it was expressed in E. coli with the enzyme activity was 53.33 U/mL, and its optimum temperature and pH was 35 °C and 7.5, respectively. The half-life of VvGBE at 35 °C was 10 h, and the enzyme was most stable at pH 9.5. When we used the recombinant enzyme to treat corn starch, the content of RS increased by 19.41%, which was higher than that achieved with other enzymes. More specially, the conversion of slowly digestible starch to RS, which was only demonstrated in chemical modification, was accomplished. The fine structure of the modified starch was further investigated. Results showed that the number of short chains (DP < 13) increased to 90.58%, and the α-1,6 linkages ratio increased from 7.19% to 15.64%. The increase of short chains and α-1,6 linkages may contribute to high RS content. This study can provide a reference for the development of modified starch with lower digestibility.

Characterization of the GH13 and GH57 glycogen branching enzymes from Petrotoga mobilis SJ95 and potential role in glycogen biosynthesis

Glycogen is a highly branched α-glucan polymer widely used as energy and carbon reserve by many microorganisms. The branches are introduced by glycogen branching enzymes (EC 2.4.1.18), that are classified into glycoside hydrolase families 13 (GH13) and 57 (GH57). Most microorganisms have typically only a single glycogen branching enzyme (gbe) gene. Only a few microorganisms carry both GH13 and GH57 gbe genes, such as Petrotoga mobilis and Mycobacterium tuberculosis. Here we report the basic characteristics of the GH13 and GH57 GBE of P. mobilis, both heterologously expressed in E. coli. The GH13 GBE has a considerably higher branching activity towards the linear α-glucan amylose, and produces a highly branched α-glucan with a high molecular weight which is very similar to glycogen. The GH57 GBE, on the contrary, makes a much smaller branched α-glucan. While the GH13 GBE acts as a classical glycogen branching enzyme involved in glycogen synthesis, the role of GH57 GBE remains unclear.

Expression and characterization of thermostable glycogen branching enzyme from Geobacillus mahadia Geo-05

The glycogen branching enzyme (EC 2.4.1.18), which catalyses the formation of α-1,6-glycosidic branch points in glycogen structure, is often used to enhance the nutritional value and quality of food and beverages. In order to be applicable in industries, enzymes that are stable and active at high temperature are much desired. Using genome mining, the nucleotide sequence of the branching enzyme gene (glgB) was extracted from the Geobacillus mahadia Geo-05 genome sequence provided by the Malaysia Genome Institute. The size of the gene is 2013 bp, and the theoretical molecular weight of the protein is 78.43 kDa. The gene sequence was then used to predict the thermostability, function and the three dimensional structure of the enzyme. The gene was cloned and overexpressed in E. coli to verify the predicted result experimentally. The purified enzyme was used to study the effect of temperature and pH on enzyme activity and stability, and the inhibitory effect by metal ion on enzyme activity. This thermostable glycogen branching enzyme was found to be most active at 55 °C, and the half-life at 60 °C and 70 °C was 24 h and 5 h, respectively. From this research, a thermostable glycogen branching enzyme was successfully isolated from Geobacillus mahadia Geo-05 by genome mining together with molecular biology technique.

Distribution of glucan-branching enzymes among prokaryotes

Glucan-branching enzyme plays an essential role in the formation of branched polysaccharides, glycogen, and amylopectin. Only one type of branching enzyme, belonging to glycoside hydrolase family 13 (GH13), is found in eukaryotes, while two types of branching enzymes (GH13 and GH57) occur in prokaryotes (Bacteria and Archaea). Both of these types are the members of protein families containing the diverse specificities of amylolytic glycoside hydrolases. Although similarities are found in the catalytic mechanism between the two types of branching enzyme, they are highly distinct from each other in terms of amino acid sequence and tertiary structure. Branching enzymes are found in 29 out of 30 bacterial phyla and 1 out of 5 archaeal phyla, often along with glycogen synthase, suggesting the existence of α-glucan production and storage in a wide range of prokaryotes. Enormous variability is observed as to which type and how many copies of branching enzyme are present depending on the phylum and, in some cases, even among species of the same genus. Such a variation may have occurred through lateral transfer, duplication, and/or differential loss of genes coding for branching enzyme during the evolution of prokaryotes.

Enzymes as Green Catalysts for Precision Macromolecular Synthesis

The present article comprehensively reviews the macromolecular synthesis using enzymes as catalysts. Among the six main classes of enzymes, the three classes, oxidoreductases, transferases, and hydrolases, have been employed as catalysts for the in vitro macromolecular synthesis and modification reactions. Appropriate design of reaction including monomer and enzyme catalyst produces macromolecules with precisely controlled structure, similarly as in vivo enzymatic reactions. The reaction controls the product structure with respect to substrate selectivity, chemo-selectivity, regio-selectivity, stereoselectivity, and choro-selectivity. Oxidoreductases catalyze various oxidation polymerizations of aromatic compounds as well as vinyl polymerizations. Transferases are effective catalysts for producing polysaccharide having a variety of structure and polyesters. Hydrolases catalyzing the bond-cleaving of macromolecules in vivo, catalyze the reverse reaction for bond forming in vitro to give various polysaccharides and functionalized polyesters. The enzymatic polymerizations allowed the first in vitro synthesis of natural polysaccharides having complicated structures like cellulose, amylose, xylan, chitin, hyaluronan, and chondroitin. These polymerizations are "green" with several respects; nontoxicity of enzyme, high catalyst efficiency, selective reactions under mild conditions using green solvents and renewable starting materials, and producing minimal byproducts. Thus, the enzymatic polymerization is desirable for the environment and contributes to "green polymer chemistry" for maintaining sustainable society.

Improved yields of cyclic nigerosylnigerose from starch by pretreatment with a thermostable branching enzyme

Cyclic nigerosylnigerose (CNN) is produced enzymatically from starch by the combined action of 6-alpha-glucosyltransferase and 3-alpha-isomaltosyltransferase. In our previous study, alpha-1,6-branching chains found in the structure of amylopectin and glycogen were shown to be favorable for CNN formation by the two enzymes. Therefore, we examined whether the introduction of alpha-1,6-branch points into starch using the action of branching enzyme (BE) could improve the yield of CNN from starch. Thermostable BE from Geobacillus stearothermophilus TC-91 was prepared as a purified recombinant protein. Pretreatment of amylose with BE considerably increased the CNN yield from 5% to 38%. When BE acted on tapioca starch, the CNN yield was elevated from 47% to 60%. Conversely, BE treatment of waxy corn starch containing very little amylose resulted in a negligible increase in CNN yield. In addition, BE exerted a beneficial effect when starch with a lower degree of hydrolysis was used as a substrate. The present results indicate that the addition of alpha-1,6-glucosidic linkages to starch using BE is an effective strategy to improve the yield of CNN from starch.

Safety evaluation of 1,4-alpha-glucan branching enzymes from Bacillus stearothermophilus and Aquifex aeolicus expressed in Bacillus subtilis

1,4-alpha-Glucan branching enzyme (BE; EC 2.4.1.18) is a key biocatalyst in the synthesis of polysaccharides, and is therefore useful in the production of food ingredients. The BEs evaluated in this study (BE-01 and BE-02) are obtained by fermentation of Bacillus subtilis expressing the BE gene from either Bacillus stearothermophilus strain TRBE14 or Aquifex aeolicus strain VF5. The safety of BE-01 and BE-02 have not been previously evaluated, and therefore, both were subjected to standard toxicological testing. In a battery of standard Salmonella typhimurium strains (TA98, TA100, TA1535, and TA1537) and in Escherichia coli WP2uvrA, both with and without metabolic activation, neither BE-01 nor BE-02 exhibited mutagenic activity. Similarly, neither was associated with clastogenic properties in Chinese hamster ovary cells in an in vitro chromosomal aberration assay. In rats, oral administration of BE-01 or BE-02 at doses of up to 15 mL/kg body weight/day (approximately 870 and 900 mg/kg body weight/day, respectively) for 13 weeks did not produce compound-related clinical signs or toxicity, changes in body weight gain, food consumption, hematology, clinical chemistry, urinalysis, organ weights, or in any gross and microscopic findings. The results of this study support the safety of BE-01 and BE-02 in food production.

The unique branching patterns of Deinococcus glycogen branching enzymes are determined by their N-terminal domains

Glycogen branching enzymes (GBE) or 1,4-alpha-glucan branching enzymes (EC 2.4.1.18) introduce alpha-1,6 branching points in alpha-glucans, e.g., glycogen. To identify structural features in GBEs that determine their branching pattern specificity, the Deinococcus geothermalis and Deinococcus radiodurans GBE (GBE(Dg) and GBE(Dr), respectively) were characterized. Compared to other GBEs described to date, these Deinococcus GBEs display unique branching patterns, both transferring relatively short side chains. In spite of their high amino acid sequence similarity (88%) the D. geothermalis enzyme had highest activity on amylose while the D. radiodurans enzyme preferred amylopectin. The side chain distributions of the products were clearly different: GBE(Dg) transferred a larger number of smaller side chains; specifically, DP5 chains corresponded to 10% of the total amount of transferred chains, versus 6.5% for GBE(Dr). GH13-type GBEs are composed of a central (beta/alpha) barrel catalytic domain and an N-terminal and a C-terminal domain. Characterization of hybrid Deinococcus GBEs revealed that the N2 modules of the N domains largely determined substrate specificity and the product branching pattern. The N2 module has recently been annotated as a carbohydrate binding module (CBM48). It appears likely that the distance between the sugar binding subsites in the active site and the CBM48 subdomain determines the average lengths of side chains transferred.

Biosynthesis of storage compounds by Rhodococcus jostii RHA1 and global identification of genes involved in their metabolism

Background

Members of the genus Rhodococcus are frequently found in soil and other natural environments and are highly resistant to stresses common in those environments. The accumulation of storage compounds permits cells to survive and metabolically adapt during fluctuating environmental conditions. The purpose of this study was to perform a genome-wide bioinformatic analysis of key genes encoding metabolism of diverse storage compounds by Rhodococcus jostii RHA1 and to examine its ability to synthesize and accumulate triacylglycerols (TAG), wax esters, polyhydroxyalkanoates (PHA), glycogen and polyphosphate (PolyP).

Results

We identified in the RHA1 genome: 14 genes encoding putative wax ester synthase/acyl-CoA:diacylglycerol acyltransferase enzymes (WS/DGATs) likely involved in TAG and wax esters biosynthesis; a total of 54 genes coding for putative lipase/esterase enzymes possibly involved in TAG and wax ester degradation; 3 sets of genes encoding PHA synthases and PHA depolymerases; 6 genes encoding key enzymes for glycogen metabolism, one gene coding for a putative polyphosphate kinase and 3 putative exopolyphosphatase genes. Where possible, key amino acid residues in the above proteins (generally in active sites, effectors binding sites or substrate binding sites) were identified in order to support gene identification. RHA1 cells grown under N-limiting conditions, accumulated TAG as the main storage compounds plus wax esters, PHA (with 3-hydroxybutyrate and 3-hydroxyvalerate monomers), glycogen and PolyP. Rhodococcus members were previously known to accumulate TAG, wax esters, PHAs and polyP, but this is the first report of glycogen accumulation in this genus.

Conclusion

RHA1 possess key genes to accumulate diverse storage compounds. Under nitrogen-limiting conditions lipids are the principal storage compounds. An extensive capacity to synthesize and metabolize storage compounds appears to contribute versatility to RHA1 in its responses to environmental stresses.

Enzymatic synthesis and properties of highly branched rice starch amylose and amylopectin cluster

We enzymatically modified rice starch to produce highly branched amylopectin and amylose and analyzed the resulting structural changes. To prepare the highly branched amylopectin cluster (HBAPC), we first treated waxy rice starch with Thermus scotoductus alpha-glucanotransferase (TSalphaGT), followed by treatment with Bacillus stearothermophilus maltogenic amylase (BSMA). Highly branched amylose (HBA) was prepared by incubating amylose with Bacillus subtilis 168 branching enzyme (BBE) and subsequently treating it with BSMA. The molecular weight of TSalphaGT-treated waxy rice starch was reduced from 8.9 x 10(8) to 1.2 x 10(5) Da, indicating that the alpha-1,4 glucosidic linkage of the segment between amylopectin clusters was hydrolyzed. Analysis of the amylopectin cluster side chains revealed that a rearrangement in the side-chain length distribution occurred. Furthermore, HBAPC and HBA were found to contain significant numbers of branched maltooligosaccharide side chains. In short, amylopectin molecules of waxy rice starch were hydrolyzed into amylopectin clusters by TSalphaGT in the enzymatic modification process, and then further branched by transglycosylation using BSMA. HBAPC and HBA showed higher water solubility and stability against retrogradation than amylopectin clusters or branched amylose. The hydrolysis rates of HBAPC and HBA by glucoamylase and alpha-amylase greatly decreased. The k cat/ K m value of glucoamylase acting on the amylopectin cluster was 45.94 s(-1)(mg/mL)(-1) and that for glucoamylase acting on HBAPC was 11.10 s(-1)(mg/mL)(-1), indicating that HBAPC was 4-fold less susceptible to glucoamylase. The k cat/ K m value for HBA was 15.90 s(-1)(mg/mL)(-1), or about three times less than that for branched amylose. The k cat/ K m values of porcine pancreatic alpha-amylase for HBAPC and HBA were 496 and 588 s(-1)(mg/mL)(-1), respectively, indicating that HBA and HBAPC are less susceptible to hydrolysis by glucoamylase and alpha-amylase. HBAPC and HBA show potential as novel glucan polymers with low digestibility and high water solubility.

Val326 of Thermoactinomyces vulgaris R-47 amylase II modulates the preference for alpha-(1,4)- and alpha-(1,6)-glycosidic linkages

Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) catalyzes not only the hydrolysis of alpha-(1,4)- and alpha-(1,6)-glycosidic linkages but also transglycosylation. The subsite +1 structure of alpha-amylase family enzymes plays important roles in substrate specificity and transglycosylation activity. We focused on the amino acid residue at the 326th position based on information on the primary structure and crystal structure, and replaced Val with Ala, Ile, or Thr. The V326A mutant favored hydrolysis of the alpha-(1,4)-glycosidic linkage compared to the wild-type enzyme. In contrast, the V326I mutant favored hydrolysis of the alpha-(1,6)-glycosidic linkage and exhibited low transglycosylation activity. In the case of the V326T mutant, the hydrolytic activity was almost identical to that of the wild-type TVA II, and the transglycosylation activity was poor. These results suggest that the volume and the hydrophobicity of the amino acid residue at the 326th position modulate both the preference for glycosidic linkages and the transglycosylation activity.

A novel branching enzyme of the GH-57 family in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1

Branching enzyme (BE) catalyzes formation of the branch points in glycogen and amylopectin by cleavage of the alpha-1,4 linkage and its subsequent transfer to the alpha-1,6 position. We have identified a novel BE encoded by an uncharacterized open reading frame (TK1436) of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. TK1436 encodes a conserved protein showing similarity to members of glycoside hydrolase family 57 (GH-57 family). At the C terminus of the TK1436 protein, two copies of a helix-hairpin-helix (HhH) motif were found. TK1436 orthologs are distributed in archaea of the order Thermococcales, cyanobacteria, some actinobacteria, and a few other bacterial species. When recombinant TK1436 protein was incubated with amylose used as the substrate, a product peak was detected by high-performance anion-exchange chromatography, eluting more slowly than the substrate. Isoamylase treatment of the reaction mixture significantly increased the level of short-chain alpha-glucans, indicating that the reaction product contained many alpha-1,6 branching points. The TK1436 protein showed an optimal pH of 7.0, an optimal temperature of 70 degrees C, and thermostability up to 90 degrees C, as determined by the iodine-staining assay. These properties were the same when a protein devoid of HhH motifs (the TK1436DeltaH protein) was used. The average molecular weight of branched glucan after reaction with the TK1436DeltaH protein was over 100 times larger than that of the starting substrate. These results clearly indicate that TK1436 encodes a structurally novel BE belonging to the GH-57 family. Identification of an overlooked BE species provides new insights into glycogen biosynthesis in microorganisms.

The concept of the alpha-amylase family: structural similarity and common catalytic mechanism

This review reconsiders the concept of the alpha-amylase family in the light of the recent wealth of information on the structures, the catalytic mechanisms, and the classification of amylases. We proposed a general concept for an enzyme family, the alpha-amylase family including most of the amylases and related enzymes in 1992, based on the structural similarity and the common catalytic mechanisms. The study on neopullulanase was the key to open the door for the formulation of the concept. We discovered a new enzyme, neopullulanase, and proved that the enzyme catalyzes both hydrolysis and transglycosylation at alpha-1,4- and alpha-1,6-glucosidic linkages by one active center. Results from a series of experiments using neopullulanase indicated that the four reactions mentioned above could be catalyzed in the same mechanism. Progress in X-ray crystallographic analysis has allowed researchers to observe the structural similarities among alpha-amylases, cyclodextrin glucanotransferases, and an isoamylase. The primary structural analyses and the secondary structural predictions also suggest a close relationship among enzymes with three-dimensional structures which catalyze one of the four reactions. They possess a catalytic (beta/alpha)8-barrel as observed in the crystal structure of alpha-amylases, cyclodextrin glucanotransferases, and an isoamylase. Two crucial points, the common catalytic mechanisms and the structural similarities among the enzymes which catalyze the four reactions, led us to propose the concept of the alpha-amylase family. We would like to point out the significance and problems of the sequence-based classification of glycosyl hydrolases. The possible catalytic mechanism of the alpha-amylase family enzyme is also described for the rational design of tailor-made artificial enzymes.

Structural features of the glycogen branching enzyme encoding genes from aspergilli

A maltose binding protein, p78, was purified to homogeneity from Aspergillus nidulans by a single column chromatography step on cross-linked amylose. The partial amino acid sequence was highly homologous to the glycogen branching enzymes (GBEs) of human and yeast, and p78 did show branching enzyme activity. The genomic gene and its cDNA encoding GBE (p78) were isolated from the A. nidulans genomic and cDNA libraries. Furthermore, a cDNA encoding A. oryzae GBE was entirely sequenced. A. nidulans GBE shared overall and significant amino acid sequence identity with GBEs from A. oryzae (83.9%), Saccharomyces cerevisiae (61.1%) and human (63.0%), and with starch branching enzymes from green plants (55-56%).

Cloning and characterization of the glycogen branching enzyme gene existing in tandem with the glycogen debranching enzyme from Pectobacterium chrysanthemi PY35

The glycogen branching enzyme gene (glgB) from Pectobacterium chrysanthemi PY35 was cloned, sequenced, and expressed in Escherichia coli. The glgB gene consisted of an open reading frame of 2196bp encoding a protein of 731 amino acids (calculated molecular weight of 83,859Da). The glgB gene is upstream of glgX and the ORF starts the ATG initiation codon and ends with the TGA stop codon at 2bp upstream of glgX. The enzyme was 43-69% sequence identical with other glycogen branching enzymes. The enzyme is the most similar to GlgB of E. coli and contained the four regions conserved among the alpha-amylase family. The glycogen branching enzyme (GlgB) was purified and the molecular weight of the enzyme was estimated to be 84kDa by SDS-PAGE. The glycogen branching enzyme was optimally active at pH 7 and 30 degrees C.

Properties and applications of starch-converting enzymes of the alpha-amylase family

Starch is a major storage product of many economically important crops such as wheat, rice, maize, tapioca, and potato. A large-scale starch processing industry has emerged in the last century. In the past decades, we have seen a shift from the acid hydrolysis of starch to the use of starch-converting enzymes in the production of maltodextrin, modified starches, or glucose and fructose syrups. Currently, these enzymes comprise about 30% of the world's enzyme production. Besides the use in starch hydrolysis, starch-converting enzymes are also used in a number of other industrial applications, such as laundry and porcelain detergents or as anti-staling agents in baking. A number of these starch-converting enzymes belong to a single family: the alpha-amylase family or family13 glycosyl hydrolases. This group of enzymes share a number of common characteristics such as a (beta/alpha)(8) barrel structure, the hydrolysis or formation of glycosidic bonds in the alpha conformation, and a number of conserved amino acid residues in the active site. As many as 21 different reaction and product specificities are found in this family. Currently, 25 three-dimensional (3D) structures of a few members of the alpha-amylase family have been determined using protein crystallization and X-ray crystallography. These data in combination with site-directed mutagenesis studies have helped to better understand the interactions between the substrate or product molecule and the different amino acids found in and around the active site. This review illustrates the reaction and product diversity found within the alpha-amylase family, the mechanistic principles deduced from structure-function relationship structures, and the use of the enzymes of this family in industrial applications.

Limited proteolysis of branching enzyme from Escherichia coli

Branching enzyme is involved in determining the structure of starch and glycogen. It catalyzes the formation of branch points by cleavage and transfer of alpha-1,4-glucan chains to alpha-1,6 branch points. Branching enzyme belongs to the amylolytic family of enzymes containing four conserved regions in a central (alpha/beta)8-barrel. Limited proteolysis of the branching enzyme from Escherichia coli (84 kDa) by proteinase K produced a truncated protein of 70-kDa, which still retained 40-60% of branching activity, depending on the type of assay used. Amino acid sequencing showed that the 70-kDa protein lacked 111 or 113 residues at the amino terminal, whereas the carboxy terminal was still intact. We purified this truncated enzyme to homogeneity and analyzed its properties. The enzyme had a three- to fourfold lower catalytic efficiency than the native enzyme, whereas the substrate specificity was unaltered. Furthermore, a branching enzyme with 112 residues deleted at the amino terminal was constructed by recombinant technology and found to have properties identical to those of the proteolyzed enzyme.