3S5Y

Pharmacological Chaperoning in Human alpha-Galactosidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.105 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The molecular basis of pharmacological chaperoning in human alpha-galactosidase

Guce, A.I.Clark, N.E.Rogich, J.J.Garman, S.C.

(2011) Chem.Biol. 18: 1521-1526

  • DOI: 10.1016/j.chembiol.2011.10.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Fabry disease patients show a deficiency in the activity of the lysosomal enzyme α-galactosidase (α-GAL or α-Gal A). One proposed treatment for Fabry disease is pharmacological chaperone therapy, where a small molecule stabilizes the α-GAL protein, l ...

    Fabry disease patients show a deficiency in the activity of the lysosomal enzyme α-galactosidase (α-GAL or α-Gal A). One proposed treatment for Fabry disease is pharmacological chaperone therapy, where a small molecule stabilizes the α-GAL protein, leading to increased enzymatic activity. Using enzyme kinetics, tryptophan fluorescence, circular dichroism, and proteolysis assays, we show that the pharmacological chaperones 1-deoxygalactonojirimycin (DGJ) and galactose stabilize the human α-GAL glycoprotein. Crystal structures of complexes of α-GAL and chaperones explain the molecular basis for the higher potency of DGJ over galactose. Using site-directed mutagenesis, we show the higher potency of DGJ results from an ionic interaction with D170. We propose that protonation of D170 in acidic conditions leads to weaker binding of DGJ. The results establish a biochemical basis for pharmacological chaperone therapy applicable to other protein misfolding diseases.


    Organizational Affiliation

    Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-galactosidase A
A, B
398Homo sapiensMutation(s): 0 
Gene Names: GLA
EC: 3.2.1.22
Find proteins for P06280 (Homo sapiens)
Go to Gene View: GLA
Go to UniProtKB:  P06280
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
A, B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
2PE
Query on 2PE

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Download CCD File 
A, B
NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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

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Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
DGJ
Query on DGJ

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Download CCD File 
A, B
(2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol
1-deoxygalactonojirimycin
C6 H13 N O4
LXBIFEVIBLOUGU-DPYQTVNSSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
XYP
Query on XYP

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Download CCD File 
A, B
BETA-D-XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
 Ligand Interaction
ACY
Query on ACY

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Download CCD File 
B
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DGJIC50: 70 nM (100) BINDINGDB
DGJKi: 39 nM BINDINGMOAD
DGJKi: 39.1 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.105 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 136.813α = 90.00
b = 182.635β = 90.00
c = 47.730γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-04
    Type: Initial release
  • Version 1.1: 2012-04-04
    Type: Structure summary