4MHX | pdb_00004mhx

Crystal Structure of Sulfamidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA.

Sidhu, N.S.Schreiber, K.Propper, K.Becker, S.Uson, I.Sheldrick, G.M.Gartner, J.Kratzner, R.Steinfeld, R.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1321-1335

  • DOI: https://doi.org/10.1107/S1399004714002739
  • Primary Citation Related Structures: 
    4MHX, 4MIV

  • PubMed Abstract: 

    Mucopolysaccharidosis type IIIA (Sanfilippo A syndrome), a fatal childhood-onset neurodegenerative disease with mild facial, visceral and skeletal abnormalities, is caused by an inherited deficiency of the enzyme N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase). More than 100 mutations in the SGSH gene have been found to reduce or eliminate its enzymatic activity. However, the molecular understanding of the effect of these mutations has been confined by a lack of structural data for this enzyme. Here, the crystal structure of glycosylated SGSH is presented at 2 Å resolution. Despite the low sequence identity between this unique N-sulfatase and the group of O-sulfatases, they share a similar overall fold and active-site architecture, including a catalytic formylglycine, a divalent metal-binding site and a sulfate-binding site. However, a highly conserved lysine in O-sulfatases is replaced in SGSH by an arginine (Arg282) that is positioned to bind the N-linked sulfate substrate. The structure also provides insight into the diverse effects of pathogenic mutations on SGSH function in mucopolysaccharidosis type IIIA and convincing evidence for the molecular consequences of many missense mutations. Further, the molecular characterization of SGSH mutations will lay the groundwork for the development of structure-based drug design for this devastating neurodegenerative disorder.


  • Organizational Affiliation
    • Department of Neuropediatrics, Faculty of Medicine, University of Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany.

Macromolecule Content 

  • Total Structure Weight: 118.54 kDa 
  • Atom Count: 7,975 
  • Modeled Residue Count: 965 
  • Deposited Residue Count: 1,020 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
N-sulphoglucosamine sulphohydrolase
A, B
510Homo sapiensMutation(s): 1 
Gene Names: SGSHHSS
EC: 3.10.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P51688 (Homo sapiens)
Explore P51688 
Go to UniProtKB:  P51688
PHAROS:  P51688
GTEx:  ENSG00000181523 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51688
Glycosylation
Glycosylation Sites: 4Go to GlyGen: P51688-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D, E, F
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
K [auth B],
L [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
G [auth A],
J [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
M [auth B],
N [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FGP
Query on FGP
A, B
L-PEPTIDE LINKINGC3 H8 N O7 PSER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.38α = 90
b = 107.9β = 104.07
c = 79.79γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2015-12-09
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2021-06-02
    Changes: Source and taxonomy, Structure summary
  • Version 2.2: 2025-03-26
    Changes: Data collection, Database references, Refinement description, Structure summary