5NPF

Crystal structure of txGH116 (beta-glucosidase from Thermoanaerobacterium xylolyticum) in complex with beta Cyclophellitol Cyclosulfate probe ME594


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.125 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

1,6-Cyclophellitol Cyclosulfates: A New Class of Irreversible Glycosidase Inhibitor.

Artola, M.Wu, L.Ferraz, M.J.Kuo, C.L.Raich, L.Breen, I.Z.Offen, W.A.Codee, J.D.C.van der Marel, G.A.Rovira, C.Aerts, J.M.F.G.Davies, G.J.Overkleeft, H.S.

(2017) ACS Cent Sci 3: 784-793

  • DOI: 10.1021/acscentsci.7b00214
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The essential biological roles played by glycosidases, coupled to the diverse therapeutic benefits of pharmacologically targeting these enzymes, provide considerable motivation for the development of new inhibitor classes. Cyclophellitol epoxides and ...

    The essential biological roles played by glycosidases, coupled to the diverse therapeutic benefits of pharmacologically targeting these enzymes, provide considerable motivation for the development of new inhibitor classes. Cyclophellitol epoxides and aziridines are recently established covalent glycosidase inactivators. Inspired by the application of cyclic sulfates as electrophilic equivalents of epoxides in organic synthesis, we sought to test whether cyclophellitol cyclosulfates would similarly act as irreversible glycosidase inhibitors. Here we present the synthesis, conformational analysis, and application of novel 1,6-cyclophellitol cyclosulfates. We show that 1,6-epi-cyclophellitol cyclosulfate (α-cyclosulfate) is a rapidly reacting α-glucosidase inhibitor whose 4C1 chair conformation matches that adopted by α-glucosidase Michaelis complexes. The 1,6-cyclophellitol cyclosulfate (β-cyclosulfate) reacts more slowly, likely reflecting its conformational restrictions. Selective glycosidase inhibitors are invaluable as mechanistic probes and therapeutic agents, and we propose cyclophellitol cyclosulfates as a valuable new class of carbohydrate mimetics for application in these directions.


    Organizational Affiliation

    Department of Bio-organic Synthesis and Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucosylceramidase
A
798Thermoanaerobacterium xylanolyticum (strain ATCC 49914 / DSM 7097 / LX-11)Mutation(s): 0 
EC: 3.2.1.45
Find proteins for F6BL85 (Thermoanaerobacterium xylanolyticum (strain ATCC 49914 / DSM 7097 / LX-11))
Go to UniProtKB:  F6BL85
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
945
Query on 945

Download SDF File 
Download CCD File 
A
[(1~{R},2~{R},3~{R},4~{S},5~{R})-2-(hydroxymethyl)-3,4,5,6-tetrakis(oxidanyl)cyclohexyl] hydrogen sulfate
C7 H14 O9 S
PDBNIRCVRHFXAD-XQCVOTFFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.125 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 178.180α = 90.00
b = 53.810β = 90.00
c = 83.300γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
Aimlessdata scaling
REFMACrefinement
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-08-23
    Type: Database references, Refinement description