Elucidation of structure and substrate-specificity of a glycoside hydrolase from family 81 and a carbohydrate binding module from family 56




Fillo, Alexander

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The degradation of carbohydrates is essential to many biological processes such as cell wall remodelling, host-pathogen defense, and energy synthesis in the form of ATP. Several of these processes utilize carbohydrate-active enzymes to accomplish these goals. Studying the degradation of polysaccharides by carbohydrate-active enzymes synthesized by microbes has allowed us to further understand biomass conversion. A portion of these polysaccharides consists of β-1,3-linked glucose (i.e. β-1,3-glucan), which is found in plants, fungi, and brown macroalgae. The hydrolysis of β-1,3-glycosidic linkages is catalyzed by β-1,3-glucanases, which are present in six different glycoside hydrolase (GH) families: 16, 17, 55, 64, 81, and 128. These enzymes play important biological roles including carbon utilization, cell wall modeling, and pathogen defense. This study focuses on a gene from Bacillus halodurans encoding for a multi-modular protein (BhLam81) consisting of a glycoside hydrolase from family 81 (BhGH81), a carbohydrate-binding module (CBM) from family 6 (BhCBM6), and a CBM from family 56 (BhCBM56). Previously, thorough structural and substrate-specific characterization has been carried out on BhCBM6. This CBM binds the non-reducing end of β-1,3-glucan. A member of CBM family 56 has been shown to recognize and bind the insoluble β-1,3-glucan, pachyman, however it is structurally uncharacterized. A glycoside hydrolase belonging to family 81 from Saccharomyces cerevisiae has been previously shown to degrade the β-1,3-glucans, laminarin and pachyman, however the structure of this enzyme was not determined. Recently, a member of GH family 81 has been structurally characterized; however, substrate-specificity was not determined in that study. Therefore, this study concentrated on two goals: Determining the substrate-specificity of BhGH81 and BhCBM56, and solving the structure of BhGH81 and BhCBM56 in order to gain insight into the molecular details of how they recognize and act on their substrate(s). The deoxyribonucleic acid (DNA) encoding for these modules were dissected by restriction digest from B. halodurans genomic DNA and recombinantly expressed in Escherichia coli (E. coli) as separate constructs. Both BhGH81 and BhCBM56 were purified and their crystal structures obtained. BhGH81 and BhCBM56 were solved to 2.5 Å resolution by single-wavelength anomalous dispersion (SAD) and to 1.7 Å resolution by multi-wavelength anomalous dispersion (MAD), respectively. In order to determine the substrate-specificity of BhGH81 and BhCBM56 and speculate on the molecular details of how they recognize and act on their substrate(s), substrate-specificity tests were combined with structural analysis for both of these modules. By using qualitative depletion assays, quantitative depletion assays, and affinity electrophoresis, it was revealed that BhCBM56 binds both insoluble and soluble β-1,3-glucan. The crystal structure of BhCBM56 revealed that it is a β-sandwich composed of two antiparallel β-sheets consisting of five β-strands each. By comparing BhCBM56 to a β-1,3-glucan binding protein from Plodia interpunctella (βGRP) a putative substrate-binding cleft on the concave side of the β-sandwich created by a platform of hydrophobic residues surrounded by several polar and charged residues was revealed. This comparison also allowed for speculation of the amino acids (W1015, H965, and D963) that are potentially essential for recognition of β-1,3-glucan substrates by BhCBM56. Activity of BhGH81 on β-1,3-glucans was confirmed by both thin-layer chromatography and product analysis using high performance anion exchange chromatography. The high performance anion exchange chromatography of BhGH81 hydrolysis suggested it has both exo and endo modes of action. The crystal structure of BhGH81 revealed that it consists of domains A, B, and C: A β-sandwich domain (A), a linker domain (B), and an (α/α)6-barrel domain (C). This structure revealed a putative substrate-binding cleft on one side of the (α/α)6-barrel with a blind canyon active site topology. It also revealed two putative catalytic residues, E542 and E546. All GHs from family 81 characterized so far, hydrolyze β-1,3-glucan in an endo acting manner. By comparing the structure of BhGH81 acquired in this study to a cellulase from Thermobifida fusca, which has an endo-processive mode of action, we can speculate that BhGH81 also has an endo-processive mode of action. The structural and biochemical analysis of BhGH81 and BhCBM56 in this study has aided in further understanding the molecular details both GH family 81 and CBM family 56 proteins, as well as the degradation of β-1,3-glucan by multimodular enzymes. Understanding these molecular details could be important for industrial applications such as, engineering a microbial platform for more efficient biofuel production.



beta-1,3-glucan, glycoside hydrolase, carbohydrate binding module