2XWE: X-ray Structure of Acid-beta-glucosidase With 5n,6s-(n'-(n- Octyl)imino)-6-thionojirimycin in the Active Site

Cyclodextrin-based host-guest chemistry has been exploited to facilitate co-crystallization of recombinant human acid beta-glucosidase (beta-glucocerebrosidase, GlcCerase) with amphiphilic bicyclic nojirimycin analogues of the sp(2)-iminosugar type. Attempts to co-crystallize GlcCerase with 5-N,6-O-[N'-(n-octyl)iminomethylidene]nojirimycin (NOI-NJ) or with 5-N,6-S-[N'-(n-octyl)iminomethylidene]-6-thionojirimycin (6S-NOI-NJ), two potent inhibitors of the enzyme with promising pharmacological chaperone activity for several Gaucher disease-associated mutations, were unsuccessful probably due to the formation of aggregates that increase the heterogeneity of the sample and affect nucleation and growth of crystals. Cyclomaltoheptaose (beta-cyclodextrin, betaCD) efficiently captures NOI-NJ and 6S-NOI-NJ in aqueous media to form inclusion complexes in which the lipophilic tail is accommodated in the hydrophobic cavity of the cyclooligosaccharide. The dissociation constant of the complex of the amphiphilic sp(2)-iminosugars with betaCD is two orders of magnitude higher than that of the corresponding complex with GlcCerase, allowing the efficient transfer of the inhibitor from the betaCD cavity to the GlcCerase active site. Enzyme-inhibitor complexes suitable for X-ray analysis were thus grown in the presence of betaCD. In contrast to what was previously observed for the complex of GlcCerase with the more basic derivative, 6-amino-6-deoxy-5-N,6-N-[N'-(n-octyl)iminomethylidene]nojirimycin (6N-NOI-NJ), the beta-anomers of both NOI-NJ and 6S-NOI-NJ were seen in the active site, even though the alpha-anomer was exclusively detected both in aqueous solution and in the corresponding betaCD:sp(2)-iminosugar complexes. Our results further suggest that cyclodextrin derivatives might serve as suitable delivery systems of amphiphilic glycosidase inhibitors in a biomedical context.
PDB ID: 2XWEDownload
MMDB ID: 93530
PDB Deposition Date: 2010/11/2
Updated in MMDB: 2011/09
Experimental Method:
x-ray diffraction
Resolution: 2.31  Å
Source Organism:
Similar Structures:
Biological Unit for 2XWE: monomeric; determined by author and by software (PISA)
Molecular Components in 2XWE
Label Count Molecule
Protein (1 molecule)
Glucosylceramidase(Gene symbol: GBA)
Molecule annotation
Chemicals (5 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB