Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 76.28 kDa 
• Atom Count: 5429 
• Modelled Residue Count: 640 
• Deposited Residue Count: 654 
• Unique protein chains: 1

4UFK

Mouse Galactocerebrosidase complexed with dideoxy-imino-lyxitol DIL

• PDB DOI: 10.2210/pdb4UFK/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2015-03-17 Released: 2015-03-25 
• Deposition Author(s): Hill, C.H., Viuff, A.H., Spratley, S.J., Salamone, S., Christensen, S.H., Read, R.J., Moriarty, N.W., Jensen, H.H., Deane, J.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.194 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 

Literature

Azasugar Inhibitors as Pharmacological Chaperones for Krabbe Disease.

Hill, C.H., Viuff, A.H., Spratley, S.J., Salamone, S., Christensen, S.H., Read, R.J., Moriarty, N.W., Jensen, H.H., Deane, J.E.

(2015) Chem Sci 6: 3075

• PubMed: 26029356 
• DOI: 10.1039/c5sc00754b
• Primary Citation of Related Structures:  
  4UFH, 4UFI, 4UFJ, 4UFK, 4UFL, 4UFM


• PubMed Abstract: 
  

Krabbe disease is a devastating neurodegenerative disorder characterized by rapid demyelination of nerve fibers. This disease is caused by defects in the lysosomal enzyme β-galactocerebrosidase (GALC), which hydrolyzes the terminal galactose from glycosphingolipids. These lipids are essential components of eukaryotic cell membranes: substrates of GALC include galactocerebroside, the primary lipid component of myelin, and psychosine, a cytotoxic metabolite. Mutations of GALC that cause misfolding of the protein may be responsive to pharmacological chaperone therapy (PCT), whereby small molecules are used to stabilize these mutant proteins, thus correcting trafficking defects and increasing residual catabolic activity in cells. Here we describe a new approach for the synthesis of galacto -configured azasugars and the characterization of their interaction with GALC using biophysical, biochemical and crystallographic methods. We identify that the global stabilization of GALC conferred by azasugar derivatives, measured by fluorescence-based thermal shift assays, is directly related to their binding affinity, measured by enzyme inhibition. X-ray crystal structures of these molecules bound in the GALC active site reveal which residues participate in stabilizing interactions, show how potency is achieved and illustrate the penalties of aza/iminosugar ring distortion. The structure-activity relationships described here identify the key physical properties required of pharmacological chaperones for Krabbe disease and highlight the potential of azasugars as stabilizing agents for future enzyme replacement therapies. This work lays the foundation for new drug-based treatments of Krabbe disease.

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Organizational Affiliation: 

Department of Haematology , Cambridge Institute for Medical Research , University of Cambridge , Cambridge CB2 0XY , UK . Email: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GALACTOCEREBROSIDASE	A	654	Mus musculus	Mutation(s): 0  Gene Names: Galc EC: 3.2.1.46
UniProt
Find proteins for P54818 (Mus musculus) Explore P54818  Go to UniProtKB:  P54818

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
LDU	D [auth A]	DIDEOXY-IMINO-LYXITOL C5 H11 N O3 OQEBIHBLFRADNM-WDCZJNDASA-N
CA	H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
LDU	Binding MOAD:  4UFK	Ki: 1.30e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.194 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 248.82	α = 90
b = 248.82	β = 90
c = 77.85	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-03-17 
• Released Date: 2015-03-25 
Deposition Author(s): Hill, C.H., Viuff, A.H., Spratley, S.J., Salamone, S., Christensen, S.H., Read, R.J., Moriarty, N.W., Jensen, H.H., Deane, J.E.

Revision History  

• Version 1.0: 2015-03-25
  Type: Initial release
  
• Version 1.1: 2015-04-01
  Changes: Derived calculations
• Version 1.2: 2015-06-10
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary