Structure of alpha-L-rhamnosidase from Dictyoglumus thermophilum

Experimental Data Snapshot

  • Resolution: 2.74 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Biochemical Characterization of the alpha-l-RhamnosidaseDtRha fromDictyoglomus thermophilum: Application to the Selective Derhamnosylation of Natural Flavonoids.

Guillotin, L.Kim, H.Traore, Y.Moreau, P.Lafite, P.Coquoin, V.Nuccio, S.de Vaumas, R.Daniellou, R.

(2019) ACS Omega 4: 1916-1922

  • DOI: https://doi.org/10.1021/acsomega.8b03186
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    α-l-Rhamnosidases are catalysts of industrial tremendous interest, but their uses are still somewhat limited by their poor thermal stabilities and selectivities. The thermophilic Dt Rha from Dictyoglomus thermophilum was cloned, and the recombinant protein was easily purified to homogeneity to afford 4.5 mg/L culture of biocatalyst. Michaelis-Menten parameters demonstrated it to be fully specific for α-l-rhamnose. Most significantly, Dt Rha demonstrated to have a stronger preference for α(1 → 2) linkage rather than α(1 → 6) linkage when removing rhamnosyl moiety from natural flavonoids. This selectivity was fully explained by the difference of binding of the corresponding substrates in the active site of the protein.

  • Organizational Affiliation

    Université d'Orléans, CNRS, ICOA, UMR 7311, Rue de Chartres, BP 6759, 45067 Orléans Cedex 2, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
944Dictyoglomus thermophilum H-6-12Mutation(s): 0 
Gene Names: DICTH_0289
Find proteins for B5YC64 (Dictyoglomus thermophilum (strain ATCC 35947 / DSM 3960 / H-6-12))
Explore B5YC64 
Go to UniProtKB:  B5YC64
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5YC64
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PGE

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
I [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
O [auth B],
P [auth B],
Q [auth B]
C6 H14 O4
Query on AE3

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
M [auth B],
N [auth B],
R [auth B]
C6 H14 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.74 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.22α = 90
b = 161.53β = 132.14
c = 124.38γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection, Database references
  • Version 1.2: 2019-09-11
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description