Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 52.42 kDa 
• Atom Count: 3754 
• Modelled Residue Count: 481 
• Deposited Residue Count: 489 
• Unique protein chains: 1

1E33

Crystal structure of an Arylsulfatase A mutant P426L

• DOI: 10.2210/pdb1E33/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Mus musculus
• Mutation(s): Yes 


• Deposited: 2000-06-06 Released: 2001-05-25 
• Deposition Author(s): von Buelow, R., Schmidt, B., Dierks, T., von Figura, K., Uson, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.250 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

Defective oligomerization of arylsulfatase a as a cause of its instability in lysosomes and metachromatic leukodystrophy.

von Bulow, R., Schmidt, B., Dierks, T., Schwabauer, N., Schilling, K., Weber, E., Uson, I., von Figura, K.

(2002) J Biol Chem 277: 9455-9461

• PubMed: 11777924 
• DOI: 10.1074/jbc.M111993200
• Primary Citation of Related Structures:  
  1E33


• PubMed Abstract: 
  

In one of the most common mutations causing metachromatic leukodystrophy, the P426L-allele of arylsulfatase A (ASA), the deficiency of ASA results from its instability in lysosomes. Inhibition of lysosomal cysteine proteinases protects the P426L-ASA and restores the sulfatide catabolism in fibroblasts of the patients. P426L-ASA, but not wild type ASA, was cleaved by purified cathepsin L at threonine 421 yielding 54- and 9-kDa fragments. X-ray crystallography at 2.5-A resolution showed that cleavage is not due to a difference in the protein fold that would expose the peptide bond following threonine 421 to proteases. Octamerization, which depends on protonation of Glu-424, was impaired for P426L-ASA. The mutation lowers the pH for the octamer/dimer equilibrium by 0.6 pH units from pH 5.8 to 5.2. A second oligomerization mutant (ASA-A464R) was generated that failed to octamerize even at pH 4.8. A464R-ASA was degraded in lysosomes to catalytically active 54-kDa intermediate. In cathepsin L-deficient fibroblasts, degradation of P426L-ASA and A464R-ASA to the 54-kDa fragment was reduced, while further degradation was blocked. This indicates that defective oligomerization of ASA allows degradation of ASA to a catalytically active 54-kDa intermediate by lysosomal cysteine proteinases, including cathepsin L. Further degradation of the 54-kDa intermediate critically depends on cathepsin L and is modified by the structure of the 9-kDa cleavage product.

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Organizational Affiliation: 

Georg-August-Universität Göttingen, Abt. Biochemie II, Heinrich-Düker-Weg 12, Göttingen 37073, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arylsulfatase A	P	489	Homo sapiens	Mutation(s): 1  Gene Names: ARSA EC: 3.1.6.8
Find proteins for P15289 (Homo sapiens) Explore P15289  Go to UniProtKB:  P15289
NIH Common Fund Data Resources
PHAROS:  P15289 GTEx:  ENSG00000100299

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	A	2		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	P	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DDZ	P	L-PEPTIDE LINKING	C3 H7 N O4		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.250 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.4	α = 90
b = 131.4	β = 90
c = 192	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-06-06 
• Released Date: 2001-05-25 
Deposition Author(s): von Buelow, R., Schmidt, B., Dierks, T., von Figura, K., Uson, I.

Revision History  

• Version 1.0: 2001-05-25
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2018-07-11
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary
• Version 3.0: 2019-04-24
  Changes: Data collection, Derived calculations, Polymer sequence
• Version 3.1: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 3.2: 2019-05-22
  Changes: Data collection, Experimental preparation, Refinement description
• Version 3.3: 2019-07-10
  Changes: Data collection
• Version 3.4: 2019-07-24
  Changes: Data collection
• Version 4.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary