2V3D

acid-beta-glucosidase with N-butyl-deoxynojirimycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.157 

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This is version 2.0 of the entry. See complete history


Literature

Crystal Structures of Complexes of N-Butyl- and N-Nonyl-Deoxynojirimycin Bound to Acid Beta-Glucosidase: Insights Into the Mechanism of Chemical Chaperone Action in Gaucher Disease.

Brumshtein, B.Greenblatt, H.M.Butters, T.D.Shaaltiel, Y.Aviezer, D.Silman, I.Futerman, A.H.Sussman, J.L.

(2007) J Biol Chem 282: 29052

  • DOI: 10.1074/jbc.M705005200
  • Primary Citation of Related Structures:  
    2V3D, 2V3E

  • PubMed Abstract: 
  • Gaucher disease is caused by mutations in the gene encoding acid beta-glucosidase (GlcCerase), resulting in glucosylceramide (GlcCer) accumulation. The only currently available orally administered treatment for Gaucher disease is N-butyl-deoxynojirimycin (Zavesca, NB-DNJ), which partially inhibits GlcCer synthesis, thus reducing levels of GlcCer accumulation ...

    Gaucher disease is caused by mutations in the gene encoding acid beta-glucosidase (GlcCerase), resulting in glucosylceramide (GlcCer) accumulation. The only currently available orally administered treatment for Gaucher disease is N-butyl-deoxynojirimycin (Zavesca, NB-DNJ), which partially inhibits GlcCer synthesis, thus reducing levels of GlcCer accumulation. NB-DNJ also acts as a chemical chaperone for GlcCerase, although at a different concentration than that required to completely inhibit GlcCer synthesis. We now report the crystal structures, at 2A resolution, of complexes of NB-DNJ and N-nonyl-deoxynojirimycin (NN-DNJ) with recombinant human GlcCerase, expressed in cultured plant cells. Both inhibitors bind at the active site of GlcCerase, with the imino sugar moiety making hydrogen bonds to side chains of active site residues. The alkyl chains of NB-DNJ and NN-DNJ are oriented toward the entrance of the active site where they undergo hydrophobic interactions. Based on these structures, we make a number of predictions concerning (i) involvement of loops adjacent to the active site in the catalytic process, (ii) the nature of nucleophilic attack by Glu-340, and (iii) the role of a conserved water molecule located in a solvent cavity adjacent to the active site. Together, these results have significance for understanding the mechanism of action of GlcCerase and the mode of GlcCerase chaperoning by imino sugars.


    Organizational Affiliation

    Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUCOSYLCERAMIDASEA, B505Homo sapiensMutation(s): 0 
Gene Names: GBAGCGLUC
EC: 3.2.1.45 (PDB Primary Data), 2.4.1 (UniProt), 3.2.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P04062 (Homo sapiens)
Explore P04062 
Go to UniProtKB:  P04062
PHAROS:  P04062
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranoseC, D4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G18638YB
GlyCosmos:  G18638YB
GlyGen:  G18638YB
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
NBV PDBBind:  2V3D Ki: 1.16e+5 (nM) from 1 assay(s)
Binding MOAD:  2V3D Ki: 1.16e+5 (nM) from 1 assay(s)
BindingDB:  2V3D Ki: 1.16e+5 (nM) from 1 assay(s)
IC50: min: 1.18e+5, max: 4.00e+5 (nM) from 7 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.993α = 90
b = 97.21β = 102.91
c = 82.406γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-08-14
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary