4MJ4

Human iduronidase apo structure P21 form

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.172 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Insights into mucopolysaccharidosis I from the structure and action of alpha-L-iduronidase.

Bie, H., Yin, J., He, X., Kermode, A.R., Goddard-Borger, E.D., Withers, S.G., James, M.N.

(2013) Nat.Chem.Biol. 9: 739-745

  • DOI: 10.1038/nchembio.1357
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Mucopolysaccharidosis type I (MPS I), caused by mutations in the gene encoding α-L-iduronidase (IDUA), is one of approximately 70 genetic disorders collectively known as the lysosomal storage diseases. To gain insight into the basis for MPS I, we cry ...

    Mucopolysaccharidosis type I (MPS I), caused by mutations in the gene encoding α-L-iduronidase (IDUA), is one of approximately 70 genetic disorders collectively known as the lysosomal storage diseases. To gain insight into the basis for MPS I, we crystallized human IDUA produced in an Arabidopsis thaliana cgl mutant. IDUA consists of a TIM barrel domain containing the catalytic site, a β-sandwich domain and a fibronectin-like domain. Structures of IDUA bound to iduronate analogs illustrate the Michaelis complex and reveal a (2,5)B conformation in the glycosyl-enzyme intermediate, which suggest a retaining double displacement reaction involving the nucleophilic Glu299 and the general acid/base Glu182. Unexpectedly, the N-glycan attached to Asn372 interacts with iduronate analogs in the active site and is required for enzymatic activity. Finally, these IDUA structures and biochemical analysis of the disease-relevant P533R mutation have enabled us to correlate the effects of mutations in IDUA to clinical phenotypes.

    Organizational Affiliation: 

    1] Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada. [2] These authors contributed equally to this work.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-L-iduronidase
A
653Homo sapiensMutation(s): 0 
Gene Names: IDUA
EC: 3.2.1.76
Find proteins for P35475 (Homo sapiens)
Go to Gene View: IDUA
Go to UniProtKB:  P35475
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL
Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN
Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA
Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.172 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.335α = 90.00
b = 70.507β = 92.10
c = 67.303γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data reduction
MxDCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2013-09-25
    Type: Database references
  • Version 1.2: 2013-11-06
    Type: Database references