PDBsum entry 3gxi

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Hydrolase PDB id
Protein chain
497 a.a. *
NAG ×4
PO4 ×63
Waters ×1679
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of acid-beta-glucosidase at ph 5.5
Structure: Glucosylceramidase. Chain: a, b, c, d. Synonym: beta-glucocerebrosidase, acid beta-glucosidase, d- n-acylsphingosine glucohydrolase, alglucerase, imiglucerase engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: gba, gc, gluc. Expressed in: cricetulus griseus. Expression_system_taxid: 10029
1.84Å     R-factor:   0.193     R-free:   0.231
Authors: R.L.Lieberman
Key ref: R.L.Lieberman et al. (2009). Effects of pH and iminosugar pharmacological chaperones on lysosomal glycosidase structure and stability. Biochemistry, 48, 4816-4827. PubMed id: 19374450
02-Apr-09     Release date:   05-May-09    
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Protein chains
Pfam   ArchSchema ?
P04062  (GLCM_HUMAN) -  Glucosylceramidase
536 a.a.
497 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Glucosylceramidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-glucosyl-N-acylsphingosine + H2O = D-glucose + N-acylsphingosine
+ H(2)O
Bound ligand (Het Group name = NAG)
matches with 62.50% similarity
+ N-acylsphingosine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   5 terms 
  Biological process     metabolic process   23 terms 
  Biochemical function     protein binding     5 terms  


Biochemistry 48:4816-4827 (2009)
PubMed id: 19374450  
Effects of pH and iminosugar pharmacological chaperones on lysosomal glycosidase structure and stability.
R.L.Lieberman, J.A.D'aquino, D.Ringe, G.A.Petsko.
Human lysosomal enzymes acid-beta-glucosidase (GCase) and acid-alpha-galactosidase (alpha-Gal A) hydrolyze the sphingolipids glucosyl- and globotriaosylceramide, respectively, and mutations in these enzymes lead to the lipid metabolism disorders Gaucher and Fabry disease, respectively. We have investigated the structure and stability of GCase and alpha-Gal A in a neutral-pH environment reflective of the endoplasmic reticulum and an acidic-pH environment reflective of the lysosome. These details are important for the development of pharmacological chaperone therapy for Gaucher and Fabry disease, in which small molecules bind mutant enzymes in the ER to enable the mutant enzyme to meet quality control requirements for lysosomal trafficking. We report crystal structures of apo GCase at pH 4.5, at pH 5.5, and in complex with the pharmacological chaperone isofagomine (IFG) at pH 7.5. We also present thermostability analysis of GCase at pH 7.4 and 5.2 using differential scanning calorimetry. We compare our results with analogous experiments using alpha-Gal A and the chaperone 1-deoxygalactonijirimycin (DGJ), including the first structure of alpha-Gal A with DGJ. Both GCase and alpha-Gal A are more stable at lysosomal pH with and without their respective iminosugars bound, and notably, the stability of the GCase-IFG complex is pH sensitive. We show that the conformations of the active site loops in GCase are sensitive to ligand binding but not pH, whereas analogous galactose- or DGJ-dependent conformational changes in alpha-Gal A are not seen. Thermodynamic parameters obtained from alpha-Gal A unfolding indicate two-state, van't Hoff unfolding in the absence of the iminosugar at neutral and lysosomal pH, and non-two-state unfolding in the presence of DGJ. Taken together, these results provide insight into how GCase and alpha-Gal A are thermodynamically stabilized by iminosugars and suggest strategies for the development of new pharmacological chaperones for lysosomal storage disorders.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21286689 M.Shanmuganathan, and P.Britz-McKibbin (2011).
Inhibitor screening of pharmacological chaperones for lysosomal β-glucocerebrosidase by capillary electrophoresis.
  Anal Bioanal Chem, 399, 2843-2853.  
21353612 T.Tsukimura, Y.Chiba, K.Ohno, S.Saito, Y.Tajima, and H.Sakuraba (2011).
Molecular mechanism for stabilization of a mutant α-galactosidase A involving M51I amino acid substitution by imino sugars.
  Mol Genet Metab, 103, 26-32.  
21138548 G.Andreotti, M.R.Guarracino, M.Cammisa, A.Correra, and M.V.Cubellis (2010).
Prediction of the responsiveness to pharmacological chaperones: lysosomal human alpha-galactosidase, a case of study.
  Orphanet J Rare Dis, 5, 36.  
  20334347 J.N.Burns, S.D.Orwig, J.L.Harris, J.D.Watkins, D.Vollrath, and R.L.Lieberman (2010).
Rescue of glaucoma-causing mutant myocilin thermal stability by chemical chaperones.
  ACS Chem Biol, 5, 477-487.  
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