PDBsum entry 2nt1

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Hydrolase PDB id
Jmol PyMol
Protein chain
497 a.a. *
NAG ×4
PO4 ×78
Waters ×1344
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Structure of acid-beta-glucosidase at neutral ph
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. Expressed in: cricetulus griseus. Expression_system_taxid: 10029. Expression_system_organ: ovary
2.30Å     R-factor:   0.178     R-free:   0.240
Authors: R.L.Lieberman,G.A.Petsko,D.Ringe
Key ref:
R.L.Lieberman et al. (2007). Structure of acid beta-glucosidase with pharmacological chaperone provides insight into Gaucher disease. Nat Chem Biol, 3, 101-107. PubMed id: 17187079 DOI: 10.1038/nchembio850
06-Nov-06     Release date:   26-Dec-06    
Go to PROCHECK summary

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     extracellular space   6 terms 
  Biological process     metabolic process   41 terms 
  Biochemical function     protein binding     5 terms  


DOI no: 10.1038/nchembio850 Nat Chem Biol 3:101-107 (2007)
PubMed id: 17187079  
Structure of acid beta-glucosidase with pharmacological chaperone provides insight into Gaucher disease.
R.L.Lieberman, B.A.Wustman, P.Huertas, A.C.Powe, C.W.Pine, R.Khanna, M.G.Schlossmacher, D.Ringe, G.A.Petsko.
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.
  Selected figure(s)  
Figure 3.
(a) Ball-and-stick representation of glycerol-bound acidic active site. (b) Ball-and-stick representation of active site seen in inh-like conformation in neutral. (c) Ball-and-stick representation of active site seen in acidic-like conformation in neutral. (d) Ball-and-stick representation of IFG-bound inh active site. Difference (F[o] - F[c]) electron density (green) is contoured at 3 and was calculated using only respective GCase coordinates. Asn396 and Trp381 are omitted for clarity. Hydrogen bonding interactions to ordered water molecules are indicated by gray dashed lines. (e) Schematic diagram of hydrogen bonding interactions involved in stabilizing IFG in the active site of GCase. Distances are in Å.
Figure 5.
(a,b) Conformation with IFG bound (a) and glycerol (GOL) bound (b). Residues in dark orange derive from PDB code 1OGS; those in yellow are acidic.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Chem Biol (2007, 3, 101-107) copyright 2007.  
  Figures were selected by an automated process.  

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.  
20824346 A.C.Muntau, and S.W.Gersting (2010).
Phenylketonuria as a model for protein misfolding diseases and for the development of next generation orphan drugs for patients with inborn errors of metabolism.
  J Inherit Metab Dis, 33, 649-658.  
20336375 J.Marshall, K.A.McEachern, W.L.Chuang, E.Hutto, C.S.Siegel, J.A.Shayman, G.A.Grabowski, R.K.Scheule, D.P.Copeland, and S.H.Cheng (2010).
Improved management of lysosomal glucosylceramide levels in a mouse model of type 1 Gaucher disease using enzyme and substrate reduction therapy.
  J Inherit Metab Dis, 33, 281-289.  
21098299 J.R.Auclair, K.J.Boggio, G.A.Petsko, D.Ringe, and J.N.Agar (2010).
Strategies for stabilizing superoxide dismutase (SOD1), the protein destabilized in the most common form of familial amyotrophic lateral sclerosis.
  Proc Natl Acad Sci U S A, 107, 21394-21399.  
20490603 J.R.Ketudat Cairns, and A.Esen (2010).
  Cell Mol Life Sci, 67, 3389-3405.  
21079602 M.D.Witte, W.W.Kallemeijn, J.Aten, K.Y.Li, A.Strijland, W.E.Donker-Koopman, A.M.van den Nieuwendijk, B.Bleijlevens, G.Kramer, B.I.Florea, B.Hooibrink, C.E.Hollak, R.Ottenhoff, R.G.Boot, G.A.van der Marel, H.S.Overkleeft, and J.M.Aerts (2010).
Ultrasensitive in situ visualization of active glucocerebrosidase molecules.
  Nat Chem Biol, 6, 907-913.  
20730629 M.Eckhardt (2010).
Pathology and current treatment of neurodegenerative sphingolipidoses.
  Neuromolecular Med, 12, 362-382.  
20148966 R.Khanna, E.R.Benjamin, L.Pellegrino, A.Schilling, B.A.Rigat, R.Soska, H.Nafar, B.E.Ranes, J.Feng, Y.Lun, A.C.Powe, D.J.Palling, B.A.Wustman, R.Schiffmann, D.J.Mahuran, D.J.Lockhart, and K.J.Valenzano (2010).
The pharmacological chaperone isofagomine increases the activity of the Gaucher disease L444P mutant form of beta-glucosidase.
  FEBS J, 277, 1618-1638.  
20505772 Y.H.Xu, Y.Sun, S.Barnes, and G.A.Grabowski (2010).
Comparative therapeutic effects of velaglucerase alfa and imiglucerase in a Gaucher disease mouse model.
  PLoS One, 5, e10750.  
19437524 B.Brumshtein, M.Aguilar-Moncayo, M.I.García-Moreno, C.Ortiz Mellet, J.M.García Fernández, I.Silman, Y.Shaaltiel, D.Aviezer, J.L.Sussman, and A.H.Futerman (2009).
6-Amino-6-deoxy-5,6-di-N-(N'-octyliminomethylidene)nojirimycin: synthesis, biological evaluation, and crystal structure in complex with acid beta-glucosidase.
  Chembiochem, 10, 1480-1485.
PDB code: 2wcg
19217815 B.Liou, and G.A.Grabowski (2009).
Participation of asparagine 370 and glutamine 235 in the catalysis by acid beta-glucosidase: the enzyme deficient in Gaucher disease.
  Mol Genet Metab, 97, 65-74.  
19833004 D.Ringe, and G.A.Petsko (2009).
What are pharmacological chaperones and why are they interesting?
  J Biol, 8, 80.  
19578116 G.H.Maegawa, M.B.Tropak, J.D.Buttner, B.A.Rigat, M.Fuller, D.Pandit, L.Tang, G.J.Kornhaber, Y.Hamuro, J.T.Clarke, and D.J.Mahuran (2009).
Identification and characterization of ambroxol as an enzyme enhancement agent for Gaucher disease.
  J Biol Chem, 284, 23502-23516.  
19521672 M.R.Landon, R.L.Lieberman, Q.Q.Hoang, S.Ju, J.M.Caaveiro, S.D.Orwig, D.Kozakov, R.Brenke, G.Y.Chuang, D.Beglov, S.Vajda, G.A.Petsko, and D.Ringe (2009).
Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase.
  J Comput Aided Mol Des, 23, 491-500.  
19374450 R.L.Lieberman, J.A.D'aquino, D.Ringe, and G.A.Petsko (2009).
Effects of pH and iminosugar pharmacological chaperones on lysosomal glycosidase structure and stability.
  Biochemistry, 48, 4816-4827.
PDB codes: 3gxd 3gxf 3gxi 3gxm 3gxn 3gxp 3gxt
19790257 T.S.Kang, and R.C.Stevens (2009).
Structural aspects of therapeutic enzymes to treat metabolic disorders.
  Hum Mutat, 30, 1591-1610.  
19717598 Y.G.Kim, J.H.Kim, and K.J.Kim (2009).
Crystal structure of the Salmonella enterica serovar typhimurium virulence factor SrfJ, a glycoside hydrolase family enzyme.
  J Bacteriol, 191, 6550-6554.
PDB code: 2wnw
19809509 Y.Sun, B.Liou, B.Quinn, H.Ran, Y.H.Xu, and G.A.Grabowski (2009).
In vivo and ex vivo evaluation of L-type calcium channel blockers on acid beta-glucosidase in Gaucher disease mouse models.
  PLoS One, 4, e7320.  
19075603 D.J.Urban, W.Zheng, O.Goker-Alpan, A.Jadhav, M.E.Lamarca, J.Inglese, E.Sidransky, and C.P.Austin (2008).
Optimization and validation of two miniaturized glucocerebrosidase enzyme assays for high throughput screening.
  Comb Chem High Throughput Screen, 11, 817-824.  
18443291 E.Ficko-Blean, K.A.Stubbs, O.Nemirovsky, D.J.Vocadlo, and A.B.Boraston (2008).
Structural and mechanistic insight into the basis of mucopolysaccharidosis IIIB.
  Proc Natl Acad Sci U S A, 105, 6560-6565.
PDB codes: 2vc9 2vca 2vcb 2vcc
18932186 G.J.Kornhaber, M.B.Tropak, G.H.Maegawa, S.J.Tuske, S.J.Coales, D.J.Mahuran, and Y.Hamuro (2008).
Isofagomine induced stabilization of glucocerebrosidase.
  Chembiochem, 9, 2643-2649.  
18328804 J.S.Shen, N.J.Edwards, Y.B.Hong, and G.J.Murray (2008).
Isofagomine increases lysosomal delivery of exogenous glucocerebrosidase.
  Biochem Biophys Res Commun, 369, 1071-1075.  
18972510 M.B.Tropak, G.J.Kornhaber, B.A.Rigat, G.H.Maegawa, J.D.Buttner, J.E.Blanchard, C.Murphy, S.J.Tuske, S.J.Coales, Y.Hamuro, E.D.Brown, and D.J.Mahuran (2008).
Identification of pharmacological chaperones for Gaucher disease and characterization of their effects on beta-glucocerebrosidase by hydrogen/deuterium exchange mass spectrometry.
  Chembiochem, 9, 2650-2662.  
18497896 M.S.Butler (2008).
Natural products to drugs: natural product-derived compounds in clinical trials.
  Nat Prod Rep, 25, 475-516.  
18254660 T.W.Mu, D.M.Fowler, and J.W.Kelly (2008).
Partial restoration of mutant enzyme homeostasis in three distinct lysosomal storage disease cell lines by altering calcium homeostasis.
  PLoS Biol, 6, e26.  
18783340 Y.Kacher, B.Brumshtein, S.Boldin-Adamsky, L.Toker, A.Shainskaya, I.Silman, J.L.Sussman, and A.H.Futerman (2008).
Acid beta-glucosidase: insights from structural analysis and relevance to Gaucher disease therapy.
  Biol Chem, 389, 1361-1369.
PDB code: 2vt0
17666401 B.Brumshtein, H.M.Greenblatt, T.D.Butters, Y.Shaaltiel, D.Aviezer, I.Silman, A.H.Futerman, and J.L.Sussman (2007).
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.
  J Biol Chem, 282, 29052-29058.
PDB codes: 2v3d 2v3e
17235342 D.A.Brooks (2007).
Getting into the fold.
  Nat Chem Biol, 3, 84-85.  
17510649 M.Molinari (2007).
N-glycan structure dictates extension of protein folding or onset of disposal.
  Nat Chem Biol, 3, 313-320.  
17644022 T.D.Butters (2007).
Gaucher disease.
  Curr Opin Chem Biol, 11, 412-418.  
17670938 W.Zheng, J.Padia, D.J.Urban, A.Jadhav, O.Goker-Alpan, A.Simeonov, E.Goldin, D.Auld, M.E.LaMarca, J.Inglese, C.P.Austin, and E.Sidransky (2007).
Three classes of glucocerebrosidase inhibitors identified by quantitative high-throughput screening are chaperone leads for Gaucher disease.
  Proc Natl Acad Sci U S A, 104, 13192-13197.  
17894779 Z.Yu, A.R.Sawkar, and J.W.Kelly (2007).
Pharmacologic chaperoning as a strategy to treat Gaucher disease.
  FEBS J, 274, 4944-4950.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.