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 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1038/nbt.2427
  • Primary Citation of Related Structures:  2XSG

  • 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 w ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CCMAN5
A, B
790Cellulosimicrobium cellulansEC: 3.2.1.24
Find proteins for M1E1E9 (Cellulosimicrobium cellulans)
Go to UniProtKB:  M1E1E9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B3P
Query on B3P

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Download CCD File 
A
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DMJ
Query on DMJ

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Download CCD File 
B
1-DEOXYMANNOJIRIMYCIN
C6 H13 N O4
LXBIFEVIBLOUGU-KVTDHHQDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.170 
  • Space Group: P 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 81.620α = 90.00
b = 91.790β = 90.00
c = 224.210γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-06
    Type: Initial release