4AQ0

Structure of the Gh92 Family Glycosyl Hydrolase Ccman5 in complex with deoxymannojirimycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 
    0.203 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.1 of the entry. See complete history


Literature

A Bacterial Glycosidase Enables Mannose-6-Phosphate Modification and Improved Cellular Uptake of Yeast-Produced Recombinant Human Lysosomal Enzymes.

Tiels, P.Baranova, E.Piens, K.De Visscher, C.Pynaert, G.Nerinckx, W.Stout, J.Fudalej, F.Hulpiau, P.Tannler, S.Geysens, S.Van Hecke, A.Valevska, A.Vervecken, W.Remaut, H.Callewaert, N.

(2012) Nat Biotechnol 30: 1225

  • DOI: https://doi.org/10.1038/nbt.2427
  • Primary Citation of Related Structures:  
    2XSG, 4AQ0

  • PubMed Abstract: 

    Lysosomal storage diseases are treated with human lysosomal enzymes produced in mammalian cells. Such enzyme therapeutics contain relatively low levels of mannose-6-phosphate, which is required to target them to the lysosomes of patient cells. Here we describe a method for increasing mannose-6-phosphate modification of lysosomal enzymes produced in yeast. We identified a glycosidase from C. cellulans that 'uncaps' N-glycans modified by yeast-type mannose-Pi-6-mannose to generate mammalian-type N-glycans with a mannose-6-phosphate substitution. Determination of the crystal structure of this glycosidase provided insight into its substrate specificity. We used this uncapping enzyme together with α-mannosidase to produce in yeast a form of the Pompe disease enzyme α-glucosidase rich in mannose-6-phosphate. Compared with the currently used therapeutic version, this form of α-glucosidase was more efficiently taken up by fibroblasts from Pompe disease patients, and it more effectively reduced cardiac muscular glycogen storage in a mouse model of the disease.


  • Organizational Affiliation

    Unit for Medical Biotechnology, Department for Molecular Biomedical Research, VIB, Ghent, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CCMAN5
A, B
790Cellulosimicrobium cellulansMutation(s): 0 
EC: 3.2.1.24
UniProt
Find proteins for M1E1E9 (Cellulosimicrobium cellulans)
Explore M1E1E9 
Go to UniProtKB:  M1E1E9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM1E1E9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free:  0.203 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.62α = 90
b = 91.79β = 90
c = 224.21γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DMJClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-06
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description