2NSX

Structure of acid-beta-glucosidase with pharmacological chaperone provides insight into Gaucher disease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of acid beta-glucosidase with pharmacological chaperone provides insight into Gaucher disease.

Lieberman, R.L.Wustman, B.A.Huertas, P.Powe, A.C.Pine, C.W.Khanna, R.Schlossmacher, M.G.Ringe, D.Petsko, G.A.

(2007) Nat.Chem.Biol. 3: 101-107

  • DOI: 10.1038/nchembio850
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Gaucher disease results from mutations in the lysosomal enzyme acid beta-glucosidase (GCase). Although enzyme replacement therapy has improved the health of some affected individuals, such as those with the prevalent N370S mutation, oral treatment wi ...

    Gaucher disease results from mutations in the lysosomal enzyme acid beta-glucosidase (GCase). Although enzyme replacement therapy has improved the health of some affected individuals, such as those with the prevalent N370S mutation, oral treatment with pharmacological chaperones may be therapeutic in a wider range of tissue compartments by restoring sufficient activity of endogenous mutant GCase. Here we demonstrate that isofagomine (IFG, 1) binds to the GCase active site, and both increases GCase activity in cell lysates and restores lysosomal trafficking in cells containing N370S mutant GCase. We also compare the crystal structures of IFG-bound GCase at low pH with those of glycerol-bound GCase at low pH and apo-GCase at neutral pH. Our data indicate that IFG induces active GCase, which is secured by interactions with Asn370. The design of small molecules that stabilize substrate-bound conformations of mutant proteins may be a general therapeutic strategy for diseases caused by protein misfolding and mistrafficking.


    Organizational Affiliation

    Structural Neurology Lab, Brigham and Women's Hospital and Harvard Medical School, 77 Ave Louis Pasteur, Boston, Massachusetts 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucosylceramidase
A, B, C, D
497Homo sapiensMutation(s): 0 
Gene Names: GBA (GC, GLUC)
EC: 3.2.1.45
Find proteins for P04062 (Homo sapiens)
Go to Gene View: GBA
Go to UniProtKB:  P04062
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IFM
Query on IFM

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Download CCD File 
B, D
5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE
Afegostat, isofagomine, (3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL
C6 H13 N O3
QPYJXFZUIJOGNX-HSUXUTPPSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NDG
Query on NDG

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Download CCD File 
A, C
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GIFKi: 5 - 23 nM (99) BINDINGDB
IFMIC50: 30 - 31000 nM (99) BINDINGDB
IFMIC50: 59 nM BINDINGMOAD
IFMIC50: 63 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 108.967α = 90.00
b = 92.216β = 110.94
c = 152.670γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
MAR345data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description