2XSG | pdb_00002xsg

Structure of the gh92 family glycosyl hydrolase ccman5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.239 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2XSG

This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 165.56 kDa 
  • Atom Count: 12,400 
  • Modeled Residue Count: 1,529 
  • Deposited Residue Count: 1,548 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CCMAN5
A, B
774Cellulosimicrobium cellulansMutation(s): 0 
EC: 3.2.1.24

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.239 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.202α = 90
b = 91.158β = 90
c = 224.523γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-12
    Type: Initial release
  • Version 1.1: 2013-02-06
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other