Distinct Characteristics of Single Starch-Binding Domain SBD1 Derived from Tandem Domains SBD1-SBD2 of Halophilic Kocuria varians Alpha-Amylase

Biochemical exploration of family GH119 reveals a single α-amylase specificity and confirms shared catalytic machinery with GH57 enzymes

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

Nanoparticles generated from a tryptophan derivative: physical characterization and anti-cancer drug delivery

Surging reports of peptide-based nanosystems and their growing potency in terms of biological utility demand for the search of newer and simpler peptide-based systems that could serve as smart templates for the development of self-assembled nanostructures. Use of simple amino acids as monomeric building blocks for synthesizing ensembles of nanostructures have gained momentum in this direction with some reports focusing on the development of nanosystems from single or modified single amino acids. In this work, we have demonstrated self-assembly and nanoparticle formation ability of a single amino acid derivative, N-alpha-(9-fluorenylmethyloxycarbonyl)-N(in)-tert-butyloxycarbonyl-L-tryptophan [Fmoc-Trp(Boc)-OH]. The nanoparticles formed by the amino acid were found to be stable to various environmental perturbations like temperature, salts and showed responsiveness to pH change. These were capable of loading and releasing different bioactive molecules and were biocompatible. These systems demonstrated high cellular uptake and doxorubicin-loaded nanoparticles were found to be more efficient in killing glioma cells as compared to the drug alone. Thus, their simple amino acid-based origin along with the ability to ferry bioactive molecules to various cells, endows them the suitability for future applications in the field of drug delivery.

Expression and Biochemical Characterization of a Thermostable Branching Enzyme from

The branching enzyme (EC 2.4.1.18) catalyzes the formation of α-1,6 branch points in starch. In this study, the <i>Geobacillus thermoglucosidans</i> gene-encoding branching enzyme was expressed in <i>Escherichia coli </i>BL21 (DE3) and the protein was isolated and characterized. <i>G. thermoglucosidans </i>branching enzyme is a thermostable enzyme with an optimal reaction temperature of nearly 60°C and a half-life at 65°C of approximately 1.1 h. The activity of the recombinant enzyme is optimal at pH 7.5, with broad stability between pH 5.5 and 9.0. Its thermostability, relatively broad pH stability and optimal temperature near the temperature at which starch begins to gelatinize may make it easy to use in industrial production. Furthermore, the enzyme is activated by Mg²⁺, Ba²⁺, K⁺ and Na⁺ in a concentration-dependent manner and dramatically inhibited by Ni²⁺ and Co²⁺. Its substrate dependence, using amylopectin as the substrate, could be adequately fitted using the Michaelis-Menten equation, yielding a<i> K</i>_m of 0.99 mg/ml. High-performance anion exchange chromatography results showed that the chain length distribution of branching enzyme-treated waxy corn starch is indistinguishable from that of the branching enzyme-treated common corn starch. This enzyme may therefore be a promising tool for the enzymatic modification of starch.

Degradation of Granular Starch by the Bacterium Microbacterium aurum Strain B8.A Involves a Modular α-Amylase Enzyme System with FNIII and CBM25 Domains

The bacterium Microbacterium aurum strain B8.A, originally isolated from a potato plant wastewater facility, is able to degrade different types of starch granules. Here we report the characterization of an unusually large, multidomain M. aurum B8.A α-amylase enzyme (MaAmyA). MaAmyA is a 1,417-amino-acid (aa) protein with a predicted molecular mass of 148 kDa. Sequence analysis of MaAmyA showed that its catalytic core is a family GH13_32 α-amylase with the typical ABC domain structure, followed by a fibronectin (FNIII) domain, two carbohydrate binding modules (CBM25), and another three FNIII domains. Recombinant expression and purification yielded an enzyme with the ability to degrade wheat and potato starch granules by introducing pores. Characterization of various truncated mutants of MaAmyA revealed a direct relationship between the presence of CBM25 domains and the ability of MaAmyA to form pores in starch granules, while the FNIII domains most likely function as stable linkers. At the C terminus, MaAmyA carries a 300-aa domain which is uniquely associated with large multidomain amylases; its function remains to be elucidated. We concluded that M. aurum B8.A employs a multidomain enzyme system to initiate degradation of starch granules via pore formation.

α-Amylase: an enzyme specificity found in various families of glycoside hydrolases

α-Amylase (EC 3.2.1.1) represents the best known amylolytic enzyme. It catalyzes the hydrolysis of α-1,4-glucosidic bonds in starch and related α-glucans. In general, the α-amylase is an enzyme with a broad substrate preference and product specificity. In the sequence-based classification system of all carbohydrate-active enzymes, it is one of the most frequently occurring glycoside hydrolases (GH). α-Amylase is the main representative of family GH13, but it is probably also present in the families GH57 and GH119, and possibly even in GH126. Family GH13, known generally as the main α-amylase family, forms clan GH-H together with families GH70 and GH77 that, however, contain no α-amylase. Within the family GH13, the α-amylase specificity is currently present in several subfamilies, such as GH13_1, 5, 6, 7, 15, 24, 27, 28, 36, 37, and, possibly in a few more that are not yet defined. The α-amylases classified in family GH13 employ a reaction mechanism giving retention of configuration, share 4-7 conserved sequence regions (CSRs) and catalytic machinery, and adopt the (β/α)8-barrel catalytic domain. Although the family GH57 α-amylases also employ the retaining reaction mechanism, they possess their own five CSRs and catalytic machinery, and adopt a (β/α)7-barrel fold. These family GH57 attributes are likely to be characteristic of α-amylases from the family GH119, too. With regard to family GH126, confirmation of the unambiguous presence of the α-amylase specificity may need more biochemical investigation because of an obvious, but unexpected, homology with inverting β-glucan-active hydrolases.