5I23

Crystal Structure of Agd31B, alpha-transglucosylase in Glycoside Hydrolase Family 31, in complex with Cyclophellitol Aziridine probe CF022


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Detection of Active Mammalian GH31 alpha-Glucosidases in Health and Disease Using In-Class, Broad-Spectrum Activity-Based Probes.

Jiang, J.Kuo, C.L.Wu, L.Franke, C.Kallemeijn, W.W.Florea, B.I.van Meel, E.van der Marel, G.A.Codee, J.D.Boot, R.G.Davies, G.J.Overkleeft, H.S.Aerts, J.M.

(2016) Acs Cent.Sci. 2: 351-358

  • DOI: 10.1021/acscentsci.6b00057
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The development of small molecule activity-based probes (ABPs) is an evolving and powerful area of chemistry. There is a major need for synthetically accessible and specific ABPs to advance our understanding of enzymes in health and disease. α-Glucos ...

    The development of small molecule activity-based probes (ABPs) is an evolving and powerful area of chemistry. There is a major need for synthetically accessible and specific ABPs to advance our understanding of enzymes in health and disease. α-Glucosidases are involved in diverse physiological processes including carbohydrate assimilation in the gastrointestinal tract, glycoprotein processing in the endoplasmic reticulum (ER), and intralysosomal glycogen catabolism. Inherited deficiency of the lysosomal acid α-glucosidase (GAA) causes the lysosomal glycogen storage disorder, Pompe disease. Here, we design a synthetic route for fluorescent and biotin-modified ABPs for in vitro and in situ monitoring of α-glucosidases. We show, through mass spectrometry, gel electrophoresis, and X-ray crystallography, that α-glucopyranose configured cyclophellitol aziridines label distinct retaining α-glucosidases including GAA and ER α-glucosidase II, and that this labeling can be tuned by pH. We illustrate a direct diagnostic application in Pompe disease patient cells, and discuss how the probes may be further exploited for diverse applications.


    Organizational Affiliation

    Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oligosaccharide 4-alpha-D-glucosyltransferase
A
836Cellvibrio japonicus (strain Ueda107)Mutation(s): 0 
Gene Names: agd31B
EC: 2.4.1.161
Find proteins for B3PEE6 (Cellvibrio japonicus (strain Ueda107))
Go to UniProtKB:  B3PEE6
Small Molecules
Ligands 4 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
EDO
Query on EDO

Download SDF File 
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
66V
Query on 66V

Download SDF File 
Download CCD File 
A
1-(8-{[(1S,2R,3S,4S,5R,6R)-2,3,4,5-tetrahydroxy-6-(hydroxymethyl)cyclohexyl]amino}octyl)triaza-1,2-dien-2-ium
C15 H31 N4 O5
KPTZFIOZQLVZBJ-SAAWNECCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.163 
  • Space Group: P 6 2 2
Unit Cell:
Length (Å)Angle (°)
a = 198.000α = 90.00
b = 198.000β = 90.00
c = 103.000γ = 120.00
Software Package:
Software NamePurpose
xia2data scaling
xia2data reduction
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-02-08 
  • Released Date: 2016-05-04 
  • Deposition Author(s): Wu, L., Davies, G.J.

Funding OrganizationLocationGrant Number
European Research CouncilUnited KingdomERC-2012-AdG-322942

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-06-22
    Type: Database references