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Biochemistry & Molecular Biology

Crystal structure of a glycoside hydrolase family 68 β-fructosyltransferase from Beijerinckia indica subsp. indica in complex with fructose

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Pages 2508-2520 | Received 12 Jun 2020, Accepted 27 Jul 2020, Published online: 04 Aug 2020

References

  • Lammens W, Le Roy K, Schroeven L, et al. Van den Ende W. Structural insights into glycoside hydrolase family 32 and 68 enzymes: functional implications. J Exp Bot. 2009;60:727–740.
  • Velázquez-Hernández ML, Baizabal-Aguirre VM, Bravo-Patiño A, et al. Microbial fructosyltransferases and the role of fructans. J Appl Microbiol. 2009;106:1763–1778.
  • Tochio T, Kadota Y, Tanaka T, et al. 1-Kestose, the smallest fructooligosaccharide component, which efficiently stimulates Faecalibacterium prausnitzii as well as Bifidobacteria in humans. Foods. 2018;7:140.
  • Koga Y, Tokunaga S, Nagano J, et al. Age-associated effect of kestose on Faecalibacterium prausnitzii and symptoms in the atopic dermatitis infants. Pediatr Res. 2016;80:844–851.
  • Tochio T, Kitaura Y, Nakamura S, et al. An alteration in the cecal microbiota composition by feeding of 1-kestose results in a marked increase in the cecal butyrate content in rats. PLoS One. 2016;11:e0166850.
  • Garron ML, Henrissat B. The continuing expansion of CAZymes and their families. Curr Opin Chem Biol. 2019;53:82–87.
  • Xie J, Cai K, Hu HX, et al. Structural analysis of the catalytic mechanism and substrate specificity of anabaena alkaline invertase InvA reveals a novel glucosidase. J Biol Chem. 2016;291:25667–25677.
  • Nagaya M, Kimura M, Gozu Y, et al. Crystal structure of a β-fructofuranosidase with high transfructosylation activity from Aspergillus kawachii. Biosci Biotechnol Biochem. 2017;81:1786–1795.
  • Becking JH. Studies on nitrogen-fixing bacteria of the genus Beijerinckia: I. Geographical and ecological distribution in soils. Plant Soil. 1961;14:49–81.
  • Tamas I, Dedysh SN, Liesack W, et al. Complete genome sequence of Beijerinckia indica subsp. indica. J Bacteriol. 2010;192:4532–4533.
  • Martínez-Fleites C, Ortíz-Lombardía M, Pons T, et al. Crystal structure of levansucrase from the Gram-negative bacterium Gluconacetobacter diazotrophicus. Biochem J. 2005;390:19–27.
  • Tonozuka T, Tamaki A, Yokoi G, et al. Crystal structure of a lactosucrose-producing enzyme, Arthrobacter sp. K-1 β-fructofuranosidase. Enzyme Microb Technol. 2012;51:359–365.
  • Ohta Y, Hatada Y, Hidaka Y, et al. Enhancing thermostability and the structural characterization of Microbacterium saccharophilum K-1 β-fructofuranosidase. Appl Microbiol Biotechnol. 2014;98:6667–6677.
  • Petersen TN, Brunak S, von Heijne G, et al. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 2011;8:785–786.
  • Kabsch W. XDS. Acta Crystallogr D Biol Crystallogr. 2010;66:125–132.
  • Evans P. Scaling and Assessment of Data Quality. Acta Crystallogr D Biol Crystallogr. 2006;62:72–82.
  • Winn MD, Ballard CC, Cowtan KD, et al. Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr. 2011;67:235–242.
  • Vagin A, Teplyakov A. Molecular replacement with MOLREP. Acta Crystallogr D Biol Crystallogr. 2010;66:22–25.
  • Langer GG, Hazledine S, Wiegels T, et al. Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 2013;69:635–641.
  • Murshudov GN, Skubák P, Lebedev AA, et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 2011;67:355–367.
  • Emsley P, Lohkamp B, Scott WG, et al. Features and development of Coot. Acta Crystallogr D Biol Crystallogr. 2010;66:486–501.
  • Lovell SC, Davis IW, Arendall WB 3rd, et al. Structure validation by Cα geometry: φ, ψ, and Cβ deviation. Proteins. 2003;50:437–450.
  • Laskowski RA, Swindells MB. LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J Chem Inf Model. 2011;51:2778–2786.
  • Wuerges J, Caputi L, Cianci M, et al. The crystal structure of Erwinia amylovora levansucrase provides a snapshot of the products of sucrose hydrolysis trapped into the active site. J Struct Biol. 2015;191:290–298.
  • Meng G, Fütterer K. Structural framework of fructosyl transfer in Bacillus subtilis levansucrase. Nat Struct Mol Biol. 2003;10:935–941.
  • Dale GE, Kostrewa D, Gsell B, et al. Crystal engineering: deletion mutagenesis of the 24 kDa fragment of the DNA gyrase B subunit from Staphylococcus aureus. Acta Crystallogr D Biol Crystallogr. 1999;55:1626–1629.
  • Derewenda ZS. Application of protein engineering to enhance crystallizability and improve crystal properties. Acta Crystallogr D Biol Crystallogr. 2010;66:604–615.
  • Caputi L, Nepogodiev SA, Malnoy M, et al. Biomolecular characterization of the levansucrase of Erwinia amylovora, a promising biocatalyst for the synthesis of fructooligosaccharides. J Agric Food Chem. 2013;61:12265–12273.
  • Strube CP, Homann A, Gamer M, et al. Polysaccharide synthesis of the levansucrase SacB from Bacillus megaterium is controlled by distinct surface motifs. J Biol Chem. 2011;286:17593–17600.
  • Yamamoto S, Iizuka M, Tanaka T, et al. The mode of synthesis of levan by Bacillus subtilis levansucrase. Agric Biol Chem. 1985;49:343–349.
  • Holm L. DALI and the persistence of protein shape. Protein Sci. 2020;29:128–140.
  • Naumoff DG. Furanosidase superfamily: search of homologues. Mol Biol. 2012;46:354–360.
  • Pijning T, Anwar MA, Böger M, et al. Crystal structure of inulosucrase from Lactobacillus: insights into the substrate specificity and product specificity of GH68 fructansucrases. J Mol Biol. 2011;412:80–93.
  • He C, Yang Y, Zhao R, et al. Rational designed mutagenesis of levansucrase from Bacillus licheniformis 8-37-0-1 for product specificity study. Appl Microbiol Biotechnol. 2018;102:3217–3228.
  • Ni D, Xu W, Zhu Y, et al. Inulin and its enzymatic production by inulosucrase: characteristics, structural features, molecular modifications and applications. Biotechnol Adv. 2019;37:306–318.
  • Porras-Domínguez JR, Ávila-Fernández Á, Miranda-Molina A, et al. Bacillus subtilis 168 levansucrase (SacB) activity affects average levan molecular weight. Carbohydr Polym. 2015;132:338–344.
  • Fujita K, Hara K, Hashimoto H, et al. Purification and some properties of beta-fructofuranosidase I from Arthrobacter sp. K-1. Agric Biol Chem. 1990;54:913–919.
  • Ortiz-Soto ME, Porras-Domínguez JR, Seibel J, et al. A close look at the structural features and reaction conditions that modulate the synthesis of low and high molecular weight fructans by levansucrases. Carbohydr Polym. 2019;219:130–142.
  • Raga-Carbajal E, Carrillo-Nava E, Costas M, et al. Size product modulation by enzyme concentration reveals two distinct levan elongation mechanisms in Bacillus subtilis levansucrase. Glycobiology. 2016;26:377–385.
  • Raga-Carbajal E, López-Munguía A, Alvarez L, et al. Understanding the transfer reaction network behind the non-processive synthesis of low molecular weight levan catalyzed by Bacillus subtilis levansucrase. Sci Rep. 2018;8:15035.
  • Ortiz-Soto ME, Porras-Domínguez JR, Seibel J, et al. A close look at the structural features and reaction conditions that modulate the synthesis of low and high molecular weight fructans by levansucrases. Carbohydr Polym. 2019;219:130–142.
  • Polsinelli I, Caliandro R, Demitri N, et al. The structure of sucrose-soaked levansucrase crystals from Erwinia tasmaniensis reveals a binding pocket for levanbiose. Int J Mol Sci. 2020;21:83.

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