5NPE

Crystal Structure of cjAgd31B (alpha-transglucosylase from Glycoside Hydrolase Family 31) in complex with beta Cyclophellitol Aziridine probe KY358


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

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
  • Structures With Same Primary Citation

  • 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

    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
Oligosaccharide 4-alpha-D-glucosyltransferaseA836Cellvibrio japonicus Ueda107Mutation(s): 0 
Gene Names: agd31BCJA_3248
EC: 2.4.1.161
Find proteins for B3PEE6 (Cellvibrio japonicus (strain Ueda107))
Explore B3PEE6 
Go to UniProtKB:  B3PEE6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
948
Query on 948

Download CCD File 
A
(1~{R},2~{S},3~{S},4~{R},5~{R},6~{R})-5-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3,4-triol
C7 H13 N O4
GPIFFOGPRPKRHS-DRYVTRLFSA-N
 Ligand Interaction
SO4
Query on SO4

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

Download CCD File 
A
OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 6 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 197α = 90
b = 197β = 90
c = 103γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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
    Changes: Database references