5NXB

Mouse galactocerebrosidase in complex with saposin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The mechanism of glycosphingolipid degradation revealed by a GALC-SapA complex structure.

Hill, C.H.Cook, G.M.Spratley, S.J.Fawke, S.Graham, S.C.Deane, J.E.

(2018) Nat Commun 9: 151-151

  • DOI: 10.1038/s41467-017-02361-y

  • PubMed Abstract: 
  • Sphingolipids are essential components of cellular membranes and defects in their synthesis or degradation cause severe human diseases. The efficient degradation of sphingolipids in the lysosome requires lipid-binding saposin proteins and hydrolytic ...

    Sphingolipids are essential components of cellular membranes and defects in their synthesis or degradation cause severe human diseases. The efficient degradation of sphingolipids in the lysosome requires lipid-binding saposin proteins and hydrolytic enzymes. The glycosphingolipid galactocerebroside is the primary lipid component of the myelin sheath and is degraded by the hydrolase β-galactocerebrosidase (GALC). This enzyme requires the saposin SapA for lipid processing and defects in either of these proteins causes a severe neurodegenerative disorder, Krabbe disease. Here we present the structure of a glycosphingolipid-processing complex, revealing how SapA and GALC form a heterotetramer with an open channel connecting the enzyme active site to the SapA hydrophobic cavity. This structure defines how a soluble hydrolase can cleave the polar glycosyl headgroups of these essential lipids from their hydrophobic ceramide tails. Furthermore, the molecular details of this interaction provide an illustration for how specificity of saposin binding to hydrolases is encoded.


    Organizational Affiliation

    Cambridge Institute for Medical Research, Department of Pathology, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Galactocerebrosidase
A, B
654Mus musculusMutation(s): 0 
Gene Names: Galc
EC: 3.2.1.46
Find proteins for P54818 (Mus musculus)
Go to UniProtKB:  P54818
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Prosaposin
C, D
87Mus musculusMutation(s): 0 
Gene Names: Psap (Sgp1)
Find proteins for Q61207 (Mus musculus)
Go to UniProtKB:  Q61207
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Download SDF File 
Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.217 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 187.183α = 90.00
b = 187.183β = 90.00
c = 360.240γ = 120.00
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing
Aimlessdata scaling
DIALSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Database references