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PDBsum entry 2v3d

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
2v3d
Jmol
Contents
Protein chain
496 a.a. *
Ligands
NAG-NAG-BMA-FUC ×2
SO4 ×8
NBV ×2
NAG
Waters ×962
* Residue conservation analysis
PDB id:
2v3d
Name: Hydrolase
Title: Acid-beta-glucosidase with n-butyl-deoxynojirimycin
Structure: Glucosylceramidase. Chain: a, b. Synonym: beta-glucocerebrosidase, acid-beta-glucosidase, d-glucosyl-n-acylsphingosine glucohydrolase, alglucerase, imiglucerase. Engineered: yes. Other_details: nb-dnj inhibitor in the active site
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: daucus carota. Expression_system_taxid: 4039
Resolution:
1.96Å     R-factor:   0.157     R-free:   0.208
Authors: B.Brumshtein,H.M.Greenblatt,T.D.Butters,Y.Shaaltiel, D.Aviezer,I.Silman,A.H.Futerman,J.L.Sussman
Key ref:
B.Brumshtein et al. (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. PubMed id: 17666401 DOI: 10.1074/jbc.M705005200
Date:
17-Jun-07     Release date:   14-Aug-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04062  (GLCM_HUMAN) -  Glucosylceramidase
Seq:
Struc:
 
Seq:
Struc:
536 a.a.
496 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 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 = BMA)
matches with 91.00% similarity
+
N-acylsphingosine
Bound ligand (Het Group name = NAG)
matches with 40.00% similarity
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  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M705005200 J Biol Chem 282:29052 (2007)
PubMed id: 17666401  
 
 
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.
B.Brumshtein, H.M.Greenblatt, T.D.Butters, Y.Shaaltiel, D.Aviezer, I.Silman, A.H.Futerman, J.L.Sussman.
 
  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 (Zavescatrade mark, 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 to 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 towards 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 Glu340, 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.
 
  Selected figure(s)  
 
Figure 2.
FIGURE 2. Comparison of binding of non-covalent inhibitors to GlcCerase. A, NN-DNJ/pGlcCerase. B, NB-DNJ/pGlcCerase. C, IFG/DG-Cerezyme. Green lines represent hydrogen bonds and red lines hydrophobic interactions. L1, loop 1 (residues 341-350); L2, loop 2 (residues 393-396); L3, loop 3 (residues 312-319). 314(B) in panel A corresponds to the side chain of a symmetrically related molecule.
Figure 4.
FIGURE 4. Conformations of the loops at the entrance to the active site. The loops in GlcCerase occur in a number of conformations, but only two are shown for clarity, in yellow and green; these conformations give the most pronounced changes in the entrance to the active site. Tyr-313, which may play a role in the catalytic mechanism, is indicated. The catalytic residues are shown as red sticks.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 29052-0) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21397496 S.Park, S.Hyun, and J.Yu (2011).
Selective α-glucosidase substrates and inhibitors containing short aromatic peptidyl moieties.
  Bioorg Med Chem Lett, 21, 2441-2444.  
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.  
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.  
19294724 A.J.Rawlings, H.Lomas, A.W.Pilling, M.J.Lee, D.S.Alonzi, J.S.Rountree, S.F.Jenkinson, G.W.Fleet, R.A.Dwek, J.H.Jones, and T.D.Butters (2009).
Synthesis and biological characterisation of novel N-alkyl-deoxynojirimycin alpha-glucosidase inhibitors.
  Chembiochem, 10, 1101-1105.  
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.  
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
18558099 D.J.Vocadlo, and G.J.Davies (2008).
Mechanistic insights into glycosidase chemistry.
  Curr Opin Chem Biol, 12, 539-555.  
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.  
18706999 M.von Itzstein (2008).
Disease-associated carbohydrate-recognising proteins and structure-based inhibitor design.
  Curr Opin Struct Biol, 18, 558-566.  
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
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.