Crystal structure of Dictyoglomus thermophilum β-D-xylosidase DtXyl unravels the structural determinants for efficient notoginsenoside R1 hydrolysis

Dictyoglomus thermophilum beta-D-xylosidase DtXyl is attractive as a potential thermostable biocatalyst able to produce biologically active ginsenosides intermediates from beta-(1,2)-D-xylosylated compounds, including Notoginsenoside-R1. DtXyl was expressed as an active N-terminal His-tagged protein, and its crystal structure was solved in presence or absence of D-xylose product. Modelling of notoginsenoside R1 in DtXyl active site led to the identification of several hydrophobic residues interacting in close contact to the substrate hydrophobic core. Unlike other residues involved in substrate binding, these residues are not conserved among GH39 xylosidase family, and their physico-chemical properties can be correlated to the efficient binding and subsequent hydrolysis of Notoginsenoside R1. (C) 2020 Elsevier B.V. and Societe Francaise de Biochimie et Biologie Moleculaire (SFBBM). All rights reserved.

Automated summary

β-D-Xylosidase DtXyl from Dictyoglomus thermophilum is a potential thermostable biocatalyst for producing biologically active ginsenosides intermediates. The crystal structure of DtXyl reveals hydrophobic residues in the active site that play a crucial role in binding and hydrolyzing Notoginsenoside R1, showing distinct properties from other residues in the GH39 xylosidase family.