6XXW | pdb_00006xxw

Structure of beta-D-Glucuronidase for Dictyoglomus thermophilum.

• PDB DOI: https://doi.org/10.2210/pdb6XXW/pdb

• Classification: HYDROLASE
• Organism(s): Dictyoglomus thermophilum H-6-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-01-28 Released: 2020-07-15 
• Deposition Author(s): Lafite, P., Daniellou, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.207 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Thioglycoligation of aromatic thiols using a natural glucuronide donor.

Kurdziel, M., Kopec, M., Paris, A., Lewinski, K., Lafite, P., Daniellou, R.

(2020) Org Biomol Chem 18: 5582-5585

• PubMed: 32671369 
• DOI: https://doi.org/10.1039/d0ob00226g
• Primary Citation Related Structures: 
  6XXW


• PubMed Abstract: 
  

  The β-d-glucuronidase DtGlcA from Dictyoglomus thermophilum was engineered to generate an active thioglycoligase that is able to catalyse the formation of numerous S-glucuronides. Its X-ray structure analysis indicated the ability of the biocatalyst to bind aromatic thiol acceptors for S-glycosylation. Noteworthily, the DtGlcA mutant was found to be the first thioligase that is able to use a natural sugar donor different from the widely used synthetic para-nitrophenyl glycosides.

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Organizational Affiliation: 
• Institut de Chimie Organique et Analytique (ICOA), Université d'Orléans/CNRS, UMR 7311, BP 6759, F-45067, Orléans Cedex 2, France. [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 71.2 kDa 
• Atom Count: 5,250 
• Modeled Residue Count: 578 
• Deposited Residue Count: 598 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucuronidase	A	598	Dictyoglomus thermophilum H-6-12	Mutation(s): 0  Gene Names: DICTH_1429 EC: 3.2.1.31
UniProt
Find proteins for B5YFE0 (Dictyoglomus thermophilum (strain ATCC 35947 / DSM 3960 / H-6-12)) Explore B5YFE0  Go to UniProtKB:  B5YFE0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	B [auth A], C [auth A], D [auth A], E [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
MPD	F [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CL	K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.207 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.13	α = 90
b = 115.82	β = 90
c = 130.54	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-15 
Deposition Author(s): Lafite, P., Daniellou, R.

Revision History  

• Version 1.0: 2020-07-15
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Changes: Database references
• Version 1.2: 2020-08-05
  Changes: Database references
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Refinement description