4NXS

Crystal structure of human alpha-galactosidase A in complex with 1-deoxygalactonojirimycin-pFPhT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5493 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular Basis of 1-Deoxygalactonojirimycin Arylthiourea Binding to Human alpha-Galactosidase A: Pharmacological Chaperoning Efficacy on Fabry Disease Mutants.

Yu, Y.Mena-Barragan, T.Higaki, K.Johnson, J.L.Drury, J.E.Lieberman, R.L.Nakasone, N.Ninomiya, H.Tsukimura, T.Sakuraba, H.Suzuki, Y.Nanba, E.Mellet, C.O.Garcia Fernandez, J.M.Ohno, K.

(2014) Acs Chem.Biol. 9: 1460-1469

  • DOI: 10.1021/cb500143h

  • PubMed Abstract: 
  • Fabry disease (FD) is an X-linked lysosomal storage disorder caused by mutations in the GLA gene often leading to missense α-galactosidase A (α-Gal A) variants that undergo premature endoplasmic reticulum-associated degradation due to folding defects ...

    Fabry disease (FD) is an X-linked lysosomal storage disorder caused by mutations in the GLA gene often leading to missense α-galactosidase A (α-Gal A) variants that undergo premature endoplasmic reticulum-associated degradation due to folding defects. We have synthesized and characterized a new family of neutral amphiphilic pharmacological chaperones, namely 1-deoxygalactonojirimycin-arylthioureas (DGJ-ArTs), capable of stabilizing α-Gal A and restoring trafficking. Binding to the enzyme is reinforced by a strong hydrogen bond involving the aryl-N'H thiourea proton and the catalytic aspartic acid acid D231 of α-Gal A, as confirmed by a 2.55 Å resolution cocrystal structure. Selected candidates enhanced α-Gal A activity and ameliorate globotriaosylceramide (Gb3) accumulation and autophagy impairments in FD cell cultures. Moreover, they acted synergistically with the proteostasis regulator 4-phenylbutyric acid, appearing to be promising leads as pharmacological chaperones for FD.


    Organizational Affiliation

    Division of Functional Genomics, Research Center for Bioscience and Technology, Tottori University , Yonago 683-8503, Japan.




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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
2OZ
Query on 2OZ

Download SDF File 
Download CCD File 
A, B
(2R,3S,4R,5S)-N-(4-fluorophenyl)-3,4,5-trihydroxy-2-(hydroxymethyl)piperidine-1-carbothioamide
C13 H17 F N2 O4 S
WPBCEOLJVINCLL-NOOOWODRSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2OZIC50: 43 - 340 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5493 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.187 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 90.783α = 90.00
b = 90.783β = 90.00
c = 217.382γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2014-07-30
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description