Crystal structure of beta-D-xylosidase from Dictyoglomus thermophilum in ligand-free form

Experimental Data Snapshot

  • Resolution: 2.72 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

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This is version 1.2 of the entry. See complete history


Crystal structure of Dictyoglomus thermophilum beta-d-xylosidase DtXyl unravels the structural determinants for efficient notoginsenoside R1 hydrolysis.

Bretagne, D.Paris, A.de Vaumas, R.Lafite, P.Daniellou, R.

(2020) Biochimie 181: 34-41

  • DOI: https://doi.org/10.1016/j.biochi.2020.11.017
  • Primary Citation of Related Structures:  
    6YYH, 6YYI

  • PubMed Abstract: 

    Dictyoglomus thermophilum β-d-xylosidase DtXyl is attractive as a potential thermostable biocatalyst able to produce biologically active ginsenosides intermediates from β-(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.

  • Organizational Affiliation

    Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans, BP 6759, Orléans, 45067, Cedex 2, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
524Dictyoglomus thermophilum H-6-12Mutation(s): 0 
Gene Names: DICTH_1792
Find proteins for B5YB78 (Dictyoglomus thermophilum (strain ATCC 35947 / DSM 3960 / H-6-12))
Explore B5YB78 
Go to UniProtKB:  B5YB78
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5YB78
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.72 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.14α = 90
b = 159.14β = 90
c = 100.15γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2020-12-09
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description