spacer
spacer

PDBsum entry 2f61

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Hydrolase PDB id
2f61
Jmol
Contents
Protein chain
497 a.a. *
Ligands
NDG
SO4 ×6
NAG-NAG
Waters ×406
* Residue conservation analysis
PDB id:
2f61
Name: Hydrolase
Title: Crystal structure of partially deglycosylated acid beta-gluc
Structure: Acid beta-glucosidase. Chain: a, b. Synonym: beta-glucocerebrosidase, glucosylceramidase, d-glu acylsphingosine glucohydrolase, alglucerase, imiglucerase. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: gba, gc. Expressed in: cricetulus griseus. Expression_system_taxid: 10029. Expression_system_cell_line: cho. Expression_system_cell: ovary
Resolution:
2.50Å     R-factor:   0.196     R-free:   0.256
Authors: R.S.Hegde,G.Grabowski
Key ref:
B.Liou et al. (2006). Analyses of Variant Acid beta-Glucosidases: EFFECTS OF GAUCHER DISEASE MUTATIONS. J Biol Chem, 281, 4242-4253. PubMed id: 16293621 DOI: 10.1074/jbc.M511110200
Date:
28-Nov-05     Release date:   27-Dec-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04062  (GLCM_HUMAN) -  Glucosylceramidase
Seq:
Struc:
 
Seq:
Struc:
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.3.2.1.45  - Glucosylceramidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-glucosyl-N-acylsphingosine + H2O = D-glucose + N-acylsphingosine
D-glucosyl-N-acylsphingosine
+ H(2)O
=
D-glucose
Bound ligand (Het Group name = NDG)
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   22 terms 
  Biochemical function     protein binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M511110200 J Biol Chem 281:4242-4253 (2006)
PubMed id: 16293621  
 
 
Analyses of Variant Acid beta-Glucosidases: EFFECTS OF GAUCHER DISEASE MUTATIONS.
B.Liou, A.Kazimierczuk, M.Zhang, C.R.Scott, R.S.Hegde, G.A.Grabowski.
 
  ABSTRACT  
 
Acid beta-glucosidase (GCase) is a 497-amino acid, membrane-associated lysosomal exo-beta-glucosidase whose defective activity leads to the Gaucher disease phenotypes. To move toward a structure/function map for disease mutations, 52 selected single amino acid substitutions were introduced into GCase, expressed in an insect cell system, purified, and characterized for basic kinetic, stability, and activator response properties. The variant GCases from Gaucher disease patients and selected variant GCases from the mouse had decreased relative k(cat) and differential effects on active site binding and/or attachment of mechanism-based covalent (conduritol B epoxide) or reversible (deoxynojirimycin derivatives) inhibitors. A defect in negatively charged phospholipid activation was present in the majority of variant GCases but was increased in two, N370S and V394L. Deficits in saposin C enhancement of k(cat) were present in variant GCases involving residues 48-122, whereas approximately 2-fold increases were obtained with the L264I GCase. About 50% of variant GCases each had wild-type or increased sensitivity to in vitro cathepsin D digestion. Mapping of these properties onto the crystal structures of GCase indicated wide dispersion of functional properties that can affect catalytic function and stability. Site-directed mutagenesis of cysteine residues showed that the disulfide bonds, Cys(4)-Cys(16) and Cys(18)-Cys(23), and a free Cys(342) were essential for activity; the free Cys(126) and Cys(248) were not. Relative k(cat) was highly sensitive to a His substitution at Arg(496) but not at Arg(495). These studies and high phylogenetic conservation indicate localized and general structural effects of Gaucher disease mutations that were not obvious from the nature of the amino acid substitution, including those predicted to be nondisruptive (e.g. Val --> Leu). These results provide initial studies for the engineering of variant GCases and, potentially, molecular chaperones for therapeutic use.
 
  Selected figure(s)  
 
Figure 2.
IC[50] values for conduritol B epoxide of GCase variants. The shaded rectangle represents the range of values for the wild type ± S.D. The ^*GCase variants had little or no enzyme activity. CBE was shown in preliminary studies to be an irreversible inhibitor of all GCase variants.
Figure 4.
Phosphatidylserine activation of GCase variants. Delipidated GCase variants were assayed in the absence and presence of phosphatidylserine (4 μm) dispersions. The enzymes were preincubated for 30 min prior to the addition of substrate.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 4242-4253) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20534487 C.P.Phenix, B.P.Rempel, K.Colobong, D.J.Doudet, M.J.Adam, L.A.Clarke, and S.G.Withers (2010).
Imaging of enzyme replacement therapy using PET.
  Proc Natl Acad Sci U S A, 107, 10842-10847.  
21098288 J.Lu, J.Chiang, R.R.Iyer, E.Thompson, C.R.Kaneski, D.S.Xu, C.Yang, M.Chen, R.J.Hodes, R.R.Lonser, R.O.Brady, and Z.Zhuang (2010).
Decreased glucocerebrosidase activity in Gaucher disease parallels quantitative enzyme loss due to abnormal interaction with TCP1 and c-Cbl.
  Proc Natl Acad Sci U S A, 107, 21665-21670.  
20490603 J.R.Ketudat Cairns, and A.Esen (2010).
β-Glucosidases.
  Cell Mol Life Sci, 67, 3389-3405.  
20937139 M.Fuller (2010).
Sphingolipids: the nexus between Gaucher disease and insulin resistance.
  Lipids Health Dis, 9, 113.  
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.  
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.  
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.  
19094956 G.A.Grabowski (2008).
Phenotype, diagnosis, and treatment of Gaucher's disease.
  Lancet, 372, 1263-1271.  
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.  
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.  
18346921 Y.H.Xu, R.Reboulet, B.Quinn, J.Huelsken, D.Witte, and G.A.Grabowski (2008).
Dependence of reversibility and progression of mouse neuronopathic Gaucher disease on acid beta-glucosidase residual activity levels.
  Mol Genet Metab, 94, 190-203.  
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
17954913 J.R.Alattia, J.E.Shaw, C.M.Yip, and G.G.Privé (2007).
Molecular imaging of membrane interfaces reveals mode of beta-glucosidase activation by saposin C.
  Proc Natl Acad Sci U S A, 104, 17394-17399.  
17187079 R.L.Lieberman, B.A.Wustman, P.Huertas, A.C.Powe, C.W.Pine, R.Khanna, M.G.Schlossmacher, D.Ringe, and G.A.Petsko (2007).
Structure of acid beta-glucosidase with pharmacological chaperone provides insight into Gaucher disease.
  Nat Chem Biol, 3, 101-107.
PDB codes: 2nsx 2nt0 2nt1
17704143 S.Abu-Baker, X.Qi, and G.A.Lorigan (2007).
Investigating the interaction of saposin C with POPS and POPC phospholipids: a solid-state NMR spectroscopic study.
  Biophys J, 93, 3480-3490.  
17644022 T.D.Butters (2007).
Gaucher disease.
  Curr Opin Chem Biol, 11, 412-418.  
17524049 Y.Shaaltiel, D.Bartfeld, S.Hashmueli, G.Baum, E.Brill-Almon, G.Galili, O.Dym, S.A.Boldin-Adamsky, I.Silman, J.L.Sussman, A.H.Futerman, and D.Aviezer (2007).
Production of glucocerebrosidase with terminal mannose glycans for enzyme replacement therapy of Gaucher's disease using a plant cell system.
  Plant Biotechnol J, 5, 579-590.
PDB code: 2v3f
17139081 B.Brumshtein, M.R.Wormald, I.Silman, A.H.Futerman, and J.L.Sussman (2006).
Structural comparison of differently glycosylated forms of acid-beta-glucosidase, the defective enzyme in Gaucher disease.
  Acta Crystallogr D Biol Crystallogr, 62, 1458-1465.
PDB code: 2j25
16945909 R.A.Steet, S.Chung, B.Wustman, A.Powe, H.Do, and S.A.Kornfeld (2006).
The iminosugar isofagomine increases the activity of N370S mutant acid beta-glucosidase in Gaucher fibroblasts by several mechanisms.
  Proc Natl Acad Sci U S A, 103, 13813-13818.  
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 codes are shown on the right.