Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 74.35 kDa 
• Atom Count: 5028 
• Modelled Residue Count: 603 
• Deposited Residue Count: 653 
• Unique protein chains: 1

4MJ4

Human iduronidase apo structure P21 form

• PDB DOI: 10.2210/pdb4MJ4/pdb
• Entry: 4MJ4 supersedes: 4JXP

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Arabidopsis thaliana
• Mutation(s): No 


• Deposited: 2013-09-03 Released: 2013-09-18 
• Deposition Author(s): Bie, H., Yin, J., He, X., Kermode, A.R., Goddard-Borger, E.D., Withers, S.G., James, M.N.G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 0.240 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

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

• PubMed: 24036510 
• DOI: 10.1038/nchembio.1357
• Primary Citation of Related Structures:  
  4KGJ, 4KGL, 4KH2, 4MJ2, 4MJ4


• 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 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-L-iduronidase	A	653	Homo sapiens	Mutation(s): 0  Gene Names: IDUA EC: 3.2.1.76
UniProt & NIH Common Fund Data Resources
Find proteins for P35475 (Homo sapiens) Explore P35475  Go to UniProtKB:  P35475
PHAROS:  P35475

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 0.240 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.335	α = 90
b = 70.507	β = 92.1
c = 67.303	γ = 90

Software Package:

Software Name	Purpose
MxDC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-09-03 
• Released Date: 2013-09-18 
Deposition Author(s): Bie, H., Yin, J., He, X., Kermode, A.R., Goddard-Borger, E.D., Withers, S.G., James, M.N.G.
• This entry supersedes: 4JXP

Revision History  

• Version 1.0: 2013-09-18
  Type: Initial release
  
• Version 1.1: 2013-09-25
  Changes: Database references
• Version 1.2: 2013-11-06
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary