5I24

Crystal Structure of Agd31B, alpha-transglucosylase in Glycoside Hydrolase Family 31, in complex with Cyclophellitol Aziridine probe CF021


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
  • Structures With Same Primary Citation

  • 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 Medical Biochemistry, 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-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
66U
Query on 66U

Download CCD File 
A
(1R,2S,3S,4R,5S,6R)-5-amino-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol
C7 H15 N O5
SWVTZDDSAFUTKS-DBTJYCMPSA-N
 Ligand Interaction
TRS
Query on TRS

Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-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: 1.85 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 6 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 197.3α = 90
b = 197.3β = 90
c = 102.9γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Source and taxonomy