5NPC

Crystal Structure of D412N nucleophile mutant cjAgd31B (alpha-transglucosylase from Glycoside Hydrolase Family 31) in complex with unreacted alpha Cyclophellitol Cyclosulfate probe ME647


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 

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 4 C 1 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

    Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain.,Fundació Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain.,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.,Department of Chemistry, University of York, Heslington, York, YO10 5DD, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oligosaccharide 4-alpha-D-glucosyltransferase
A
835Cellvibrio japonicus (strain Ueda107)Mutation(s): 1 
Gene Names: agd31B
EC: 2.4.1.161
Find proteins for B3PEE6 (Cellvibrio japonicus (strain Ueda107))
Go to UniProtKB:  B3PEE6
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
94E
Query on 94E

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Download CCD File 
A
(3~{a}~{R},4~{R},5~{S},6~{R},7~{R},7~{a}~{S})-7-(hydroxymethyl)-2,2-bis(oxidanylidene)-3~{a},4,5,6,7,7~{a}-hexahydrobenzo[d][1,3,2]dioxathiole-4,5,6-triol
C7 H12 O8 S
ZCXRKCCKXOHKLN-XQCVOTFFSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
OXL
Query on OXL

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Download CCD File 
A
OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 
  • Space Group: P 6 2 2
Unit Cell:
Length (Å)Angle (°)
a = 197.140α = 90.00
b = 197.140β = 90.00
c = 102.780γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
xia2data reduction
Aimlessdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-04-16 
  • Released Date: 2017-08-09 
  • Deposition Author(s): Wu, L., Davies, G.J.

Revision History 

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