PDBsum entry 2v3e

Hydrolase

PDB id: 2v3e

Contents

Protein chain

498 a.a. *

Ligands

NAG-NAG-BMA-FUC ×2

NND ×2

PO4 ×2

NAG

Waters ×1004

* Residue conservation analysis

PDB id:

2v3e

Name:

Hydrolase

Title:

Acid-beta-glucosidase with n-nonyl-deoxynojirimycin

Structure:

Glucosylceramidase. Chain: a, b. Synonym: beta-glucocerebrosidase, acid-beta-glucosidase, d-glucosyl- n-acylsphingosine glucohydrolase, alglucerase, imiglucerase. Engineered: yes. Other_details: nn-dnj in the active site

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: daucus carota. Expression_system_taxid: 4039

Resolution:

2.00Å R-factor: 0.163 R-free: 0.220

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: 21-Aug-07

Protein chains

P04062  (GLCM_HUMAN) -  Lysosomal acid glucosylceramidase from Homo sapiens

Seq: 536 a.a.

Struc: 498 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: E.C.2.4.1.- - ?????
• Enzyme class 3: E.C.3.2.1.- - ?????
• Enzyme class 4: E.C.3.2.1.45 - glucosylceramidase.
• Reaction: a beta-D-glucosyl-(1<->1')-N-acylsphing-4-enine + H2O = an N-acylsphing- 4-enine + D-glucose

beta-D-glucosyl-(1<->1')-N-acylsphing-4-enine + H2O = N-acylsphing- 4-enine + D-glucose (Bound ligand (Het Group name = BMA) matches with 91.67% similarity)

• Enzyme class 5: E.C.3.2.1.46 - galactosylceramidase.
• Reaction: a beta-D-galactosyl-(1<->1')-N-acylsphing-4-enine + H2O = an N-acylsphing-4-enine + D-galactose

beta-D-galactosyl-(1<->1')-N-acylsphing-4-enine + H2O = N-acylsphing-4-enine + D-galactose (Bound ligand (Het Group name = BMA) matches with 91.67% similarity)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added 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.