5FQL

Insights into Hunter syndrome from the structure of iduronate-2- sulfatase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

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This is version 3.0 of the entry. See complete history


Literature

Insights into Hunter syndrome from the structure of iduronate-2-sulfatase.

Demydchuk, M.Hill, C.H.Zhou, A.Bunkoczi, G.Stein, P.E.Marchesan, D.Deane, J.E.Read, R.J.

(2017) Nat Commun 8: 15786-15786

  • DOI: https://doi.org/10.1038/ncomms15786
  • Primary Citation of Related Structures:  
    5FQL

  • PubMed Abstract: 

    Hunter syndrome is a rare but devastating childhood disease caused by mutations in the IDS gene encoding iduronate-2-sulfatase, a crucial enzyme in the lysosomal degradation pathway of dermatan sulfate and heparan sulfate. These complex glycosaminoglycans have important roles in cell adhesion, growth, proliferation and repair, and their degradation and recycling in the lysosome is essential for cellular maintenance. A variety of disease-causing mutations have been identified throughout the IDS gene. However, understanding the molecular basis of the disease has been impaired by the lack of structural data. Here, we present the crystal structure of human IDS with a covalently bound sulfate ion in the active site. This structure provides essential insight into multiple mechanisms by which pathogenic mutations interfere with enzyme function, and a compelling explanation for severe Hunter syndrome phenotypes. Understanding the structural consequences of disease-associated mutations will facilitate the identification of patients that may benefit from specific tailored therapies.


  • Organizational Affiliation

    Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IDURONATE-2-SULFATASE525Homo sapiensMutation(s): 0 
EC: 3.1.6.13
UniProt & NIH Common Fund Data Resources
Find proteins for P22304 (Homo sapiens)
Explore P22304 
Go to UniProtKB:  P22304
PHAROS:  P22304
GTEx:  ENSG00000010404 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22304
Glycosylation
Glycosylation Sites: 7Go to GlyGen: P22304-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
B, C, E
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, F
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ALS
Query on ALS
A
L-PEPTIDE LINKINGC3 H7 N O7 SALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.05α = 90
b = 71.05β = 90
c = 285.879γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-06-21
    Changes: Database references
  • Version 2.0: 2019-10-23
    Changes: Atomic model, Data collection, Derived calculations, Other
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary