Structural Insight into a Yeast Maltase—The BaAG2 from Blastobotrys adeninivorans with Transglycosylating Activity

An early-diverged yeast, Blastobotrys (Arxula) adeninivorans (Ba), has biotechnological potential due to nutritional versatility, temperature tolerance, and production of technologically applicable enzymes. We have biochemically characterized from the Ba type strain (CBS 8244) the GH13-family maltase BaAG2 with efficient transglycosylation activity on maltose. In the current study, transglycosylation of sucrose was studied in detail. The chemical entities of sucrose-derived oligosaccharides were determined using nuclear magnetic resonance. Several potentially prebiotic oligosaccharides with α-1,1, α-1,3, α-1,4, and α-1,6 linkages were disclosed among the products. Trisaccharides isomelezitose, erlose, and theanderose, and disaccharides maltulose and trehalulose were dominant transglycosylation products. To date no structure for yeast maltase has been determined. Structures of the BaAG2 with acarbose and glucose in the active center were solved at 2.12 and 2.13 Å resolution, respectively. BaAG2 exhibited a catalytic domain with a (β/α)8-barrel fold and Asp216, Glu274, and Asp348 as the catalytic triad. The fairly wide active site cleft contained water channels mediating substrate hydrolysis. Next to the substrate-binding pocket an enlarged space for potential binding of transglycosylation acceptors was identified. The involvement of a Glu (Glu309) at subsite +2 and an Arg (Arg233) at subsite +3 in substrate binding was shown for the first time for α-glucosidases.

[1]  M. K. Maiti,et al.  Yeasts of the Blastobotrys genus are promising platform for lipid-based fuels and oleochemicals production , 2021, Applied Microbiology and Biotechnology.

[2]  Shukun Tang,et al.  Proteogenomics Study of Blastobotrys adeninivorans TMCC 70007-A Dominant Yeast in the Fermentation Process of Pu-erh Tea. , 2021, Journal of proteome research.

[3]  C. V. Iancu,et al.  Crystal structures of non-oxidative decarboxylases reveal a new mechanism of action with a catalytic dyad and structural twists , 2021, Scientific Reports.

[4]  R. Shoeman,et al.  BioMAX – the first macromolecular crystallography beamline at MAX IV Laboratory , 2020, Journal of synchrotron radiation.

[5]  F. Plou,et al.  Molecular characterization and heterologous expression of two α-glucosidases from Metschnikowia spp, both producers of honey sugars , 2020, Microbial Cell Factories.

[6]  T. Miyazaki,et al.  Structure–function analysis of silkworm sucrose hydrolase uncovers the mechanism of substrate specificity in GH13 subfamily 17 exo-α-glucosidases , 2020, The Journal of Biological Chemistry.

[7]  T. Alamäe,et al.  Characterization of a Maltase from an Early-Diverged Non-Conventional Yeast Blastobotrys adeninivorans , 2019, International journal of molecular sciences.

[8]  S. Davis,et al.  Considerations when using alpha-glucosidase inhibitors in the treatment of type 2 diabetes , 2019, Expert opinion on pharmacotherapy.

[9]  Fadia V. Cervantes,et al.  Efficient production of isomelezitose by a glucosyltransferase activity in Metschnikowia reukaufii cell extracts , 2019, Microbial biotechnology.

[10]  C. Neuvéglise,et al.  Blastobotrys adeninivorans and B. raffinosifermentans, two sibling yeast species which accumulate lipids at elevated temperatures and from diverse sugars , 2019, Biotechnology for Biofuels.

[11]  Guo-Ping Zhou,et al.  Influence of Calcium Ions on the Thermal Characteristics of α-amylase from Thermophilic Anoxybacillus sp. GXS-BL , 2019, Protein and peptide letters.

[12]  J. Marín-Navarro,et al.  Amylases and related glycoside hydrolases with transglycosylation activity used for the production of isomaltooligosaccharides , 2018, Amylase.

[13]  T. Alamäe,et al.  Genome Mining of Non-Conventional Yeasts: Search and Analysis of MAL Clusters and Proteins , 2018, Genes.

[14]  M. Yao,et al.  Function and structure of GH13_31 α‐glucosidase with high α‐(1→4)‐glucosidic linkage specificity and transglucosylation activity , 2018, FEBS letters.

[15]  Christopher J. Williams,et al.  MolProbity: More and better reference data for improved all‐atom structure validation , 2018, Protein science : a publication of the Protein Society.

[16]  Lukas Zimmermann,et al.  A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. , 2017, Journal of molecular biology.

[17]  T. Alamäe,et al.  A Highly Active Endo-Levanase BT1760 of a Dominant Mammalian Gut Commensal Bacteroides thetaiotaomicron Cleaves Not Only Various Bacterial Levans, but Also Levan of Timothy Grass , 2017, PloS one.

[18]  G. Kunze,et al.  Blastobotrys (Arxula) adeninivorans: a promising alternative yeast for biotechnology and basic research , 2016, Yeast.

[19]  T. Alamäe,et al.  Maltase protein of Ogataea (Hansenula) polymorpha is a counterpart to the resurrected ancestor protein ancMALS of yeast maltases and isomaltases , 2016, Yeast.

[20]  F. Plou,et al.  Molecular characterization and heterologous expression of a Xanthophyllomyces dendrorhous α-glucosidase with potential for prebiotics production , 2015, Applied Microbiology and Biotechnology.

[21]  G. Kunze,et al.  Three New Cutinases from the Yeast Arxula adeninivorans That Are Suitable for Biotechnological Applications , 2015, Applied and Environmental Microbiology.

[22]  M. Yao,et al.  Structural analysis of the α-glucosidase HaG provides new insights into substrate specificity and catalytic mechanism. , 2015, Acta crystallographica. Section D, Biological crystallography.

[23]  G. Kunze,et al.  A novel enzymatic approach in the production of food with low purine content using Arxula adeninivorans endogenous and recombinant purine degradative enzymes , 2015, Bioengineered.

[24]  T. Alamäe,et al.  High-Throughput Assay of Levansucrase Variants in Search of Feasible Catalysts for the Synthesis of Fructooligosaccharides and Levan , 2014, Molecules.

[25]  Paul P Jung,et al.  The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest , 2014, Biotechnology for Biofuels.

[26]  Pedro M. Coutinho,et al.  The carbohydrate-active enzymes database (CAZy) in 2013 , 2013, Nucleic Acids Res..

[27]  K. Verstrepen,et al.  Reconstruction of Ancestral Metabolic Enzymes Reveals Molecular Mechanisms Underlying Evolutionary Innovation through Gene Duplication , 2012, PLoS biology.

[28]  S. Parasuraman,et al.  Protein data bank , 2012, Journal of pharmacology & pharmacotherapeutics.

[29]  Toshiyuki Sato,et al.  Purification, characterization, and gene identification of an α-glucosyl transfer enzyme, a novel type α-glucosidase from Xanthomonas campestris WU-9701 , 2012 .

[30]  R. Consonni,et al.  NMR characterization of saccharides in Italian honeys of different floral sources. , 2012, Journal of agricultural and food chemistry.

[31]  P. Zwart,et al.  Towards automated crystallographic structure refinement with phenix.refine , 2012, Acta crystallographica. Section D, Biological crystallography.

[32]  Keizo Yamamoto,et al.  Steric hindrance by 2 amino acid residues determines the substrate specificity of isomaltase from Saccharomyces cerevisiae. , 2011, Journal of bioscience and bioengineering.

[33]  Olof Svensson,et al.  ISPyB: an information management system for synchrotron macromolecular crystallography , 2011, Bioinform..

[34]  D. Higgins,et al.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.

[35]  M. Okuyama,et al.  Calcium Ion-Dependent Increase in Thermostability of Dextran Glucosidase from Streptococcus mutans , 2011, Bioscience, biotechnology, and biochemistry.

[36]  Keizo Yamamoto,et al.  Crystal structures of isomaltase from Saccharomyces cerevisiae and in complex with its competitive inhibitor maltose , 2010, The FEBS journal.

[37]  P. Schweitzer,et al.  HPLC sugar profiles of Algerian honeys , 2010 .

[38]  Ana C. Soria,et al.  Gas chromatographic–mass spectrometric characterisation of tri- and tetrasaccharides in honey , 2010 .

[39]  Vincent B. Chen,et al.  PHENIX: a comprehensive Python-based system for macromolecular structure solution , 2010, Acta crystallographica. Section D, Biological crystallography.

[40]  Olof Svensson,et al.  EDNA: a framework for plugin-based applications applied to X-ray experiment online data analysis. , 2009, Journal of synchrotron radiation.

[41]  M. Piontek,et al.  Atan1p—an extracellular tannase from the dimorphic yeast Arxula adeninivorans: molecular cloning of the ATAN1 gene and characterization of the recombinant enzyme , 2009, Yeast.

[42]  Brandi L. Cantarel,et al.  The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics , 2008, Nucleic Acids Res..

[43]  Y. Matsuura,et al.  Substrate recognition mechanism of alpha-1,6-glucosidic linkage hydrolyzing enzyme, dextran glucosidase from Streptococcus mutans. , 2008, Journal of molecular biology.

[44]  B. Nichols,et al.  Human intestinal maltase-glucoamylase: crystal structure of the N-terminal catalytic subunit and basis of inhibition and substrate specificity. , 2008, Journal of molecular biology.

[45]  F. Plou,et al.  Transformation of maltose into prebiotic isomaltooligosaccharides by a novel α-glucosidase from Xantophyllomyces dendrorhous , 2007 .

[46]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[47]  Kunihiko Watanabe,et al.  Molecular determinants of substrate recognition in thermostable alpha-glucosidases belonging to glycoside hydrolase family 13. , 2007, Journal of biochemistry.

[48]  J. A. Jorge,et al.  A novel α-glucosidase from Chaetomium thermophilum var. coprophilum that converts maltose into trehalose: Purification and partial characterisation of the enzyme , 2006 .

[49]  M. Harding,et al.  Small revisions to predicted distances around metal sites in proteins. , 2006, Acta crystallographica. Section D, Biological crystallography.

[50]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[51]  G. Kunze,et al.  Characterization of the AINV gene and the encoded invertase from the dimorphic yeast Arxula adeninivorans , 2004, Antonie van Leeuwenhoek.

[52]  Adam Godzik,et al.  The importance of alignment accuracy for molecular replacement. , 2004, Acta crystallographica. Section D, Biological crystallography.

[53]  J. Kastrup,et al.  Crystal structure of sucrose phosphorylase from Bifidobacterium adolescentis. , 2004, Biochemistry.

[54]  Tetsuo Kobayashi,et al.  Novel α-Glucosidase from Aspergillus nidulans with Strong Transglycosylation Activity , 2002, Applied and Environmental Microbiology.

[55]  M. Gajhede,et al.  Crystal structures of amylosucrase from Neisseria polysaccharea in complex with D-glucose and the active site mutant Glu328Gln in complex with the natural substrate sucrose. , 2001, Biochemistry.

[56]  R. Wierenga,et al.  The TIM‐barrel fold: a versatile framework for efficient enzymes , 2001, FEBS letters.

[57]  J. Newell,et al.  Unraveling the Function of Glycosyltransferases in Streptococcus thermophilus Sfi6 , 1999, Journal of bacteriology.

[58]  Y. Matsuura,et al.  Three-dimensional structure of Pseudomonas isoamylase at 2.2 A resolution. , 1998, Journal of molecular biology.

[59]  B. Svensson,et al.  Molecular structure of a barley alpha-amylase-inhibitor complex: implications for starch binding and catalysis. , 1998, Journal of molecular biology.

[60]  B Henrissat,et al.  Structural and sequence-based classification of glycoside hydrolases. , 1997, Current opinion in structural biology.

[61]  A. Brzozowski,et al.  Structure of the Aspergillus oryzae alpha-amylase complexed with the inhibitor acarbose at 2.0 A resolution. , 1997, Biochemistry.

[62]  K. Watanabe,et al.  The refined crystal structure of Bacillus cereus oligo-1,6-glucosidase at 2.0 A resolution: structural characterization of proline-substitution sites for protein thermostabilization. , 1997, Journal of molecular biology.

[63]  G. Kunze,et al.  Expression of the Arxula adeninivorans glucoamylase gene in Kluyveromyces lactis , 1996, Applied Microbiology and Biotechnology.

[64]  K. Adler,et al.  Temperature-dependent dimorphism of the yeastArxula adeninivorans Ls3 , 1995, Antonie van Leeuwenhoek.

[65]  S. Withers,et al.  The structure of human pancreatic α‐amylase at 1.8 Å resolution and comparisons with related enzymes , 1995, Protein science : a publication of the Protein Society.

[66]  R. Huber,et al.  Crystal structure of calcium-depleted Bacillus licheniformis alpha-amylase at 2.2 A resolution. , 1995, Journal of molecular biology.

[67]  L. Dijkhuizen,et al.  X-ray structure of cyclodextrin glycosyltransferase complexed with acarbose. Implications for the catalytic mechanism of glycosidases. , 1994, Biochemistry.

[68]  F. Studier,et al.  Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. , 1986, Journal of molecular biology.

[69]  Y. Matsuura,et al.  Structure and possible catalytic residues of Taka-amylase A. , 1982, Journal of biochemistry.

[70]  S. Chiba,et al.  A New Trisaccharide, 6F-α-D-Glucosyl-sucrose, Synthesized by Trans-glucosylation Reaction of Brewer's Yeast α-Glucosidase , 1979 .

[71]  M. Takizawa,et al.  Characterization and expression analysis of a maltose-utilizing (MAL) cluster in Aspergillus oryzae. , 2010, Fungal genetics and biology : FG & B.

[72]  S. Tabata,et al.  Val216 decides the substrate specificity of alpha-glucosidase in Saccharomyces cerevisiae. , 2004, European journal of biochemistry.

[73]  W. Delano The PyMOL Molecular Graphics System , 2002 .

[74]  Š. Janeček,et al.  Relationship of sequence and structure to specificity in the alpha-amylase family of enzymes. , 2001, Biochimica et biophysica acta.

[75]  M. Kim,et al.  Comparative study of the inhibition of alpha-glucosidase, alpha-amylase, and cyclomaltodextrin glucanosyltransferase by acarbose, isoacarbose, and acarviosine-glucose. , 1999, Archives of biochemistry and biophysics.

[76]  H. Verachtert,et al.  Localization and Characterization of alpha-Glucosidase Activity in Brettanomyces lambicus. , 1993, Applied and environmental microbiology.