Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 66043.10 
• Atom Count: 4601 
• Residue Count: 606 
• Unique protein chains: 2

1APY

HUMAN ASPARTYLGLUCOSAMINIDASE

• DOI: 10.2210/pdb1APY/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens


• Deposited: 1995-06-14 Released: 1996-12-23 
• Deposition Author(s): Rouvinen, J., Oinonen, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.224 
• R-Value Work: 0.169 

Literature

Three-dimensional structure of human lysosomal aspartylglucosaminidase.

Oinonen, C., Tikkanen, R., Rouvinen, J., Peltonen, L.

(1995) Nat.Struct.Mol.Biol. 2: 1102-1108

• PubMed: 8846222 
• Primary Citation of Related Structures:  
  1APZ
• Also Cited By: 2ZAL, 1SEO


• PubMed Abstract: 
  

The high resolution crystal structure of human lysosomal aspartylglucosaminidase (AGA) has been determined. This lysosomal enzyme is synthesized as a single polypeptide precursor, which is immediately post-translationally cleaved into alpha- and beta-subunits. Two alpha- and beta-chains are found to pack together forming the final heterotetrameric structure. The catalytically essential residue, the N-terminal threonine of the beta-chain is situated in the deep pocket of the funnel-shaped active site. On the basis of the structure of the enzyme-product complex we present a catalytic mechanism for this lysosomal enzyme with an exceptionally high pH optimum. The three-dimensional structure also allows the prediction of the structural consequences of human mutations resulting in aspartylglucosaminuria (AGU), a lysosomal storage disease.

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Related Citations: 

• Large-Scale Purification and Preliminary X-Ray Diffraction Studies of Human Aspartylglucosaminidase
  Tikkanen, R.,Rouvinen, J.,Torronen, A.,Kalkkinen, N.,Peltonen, L.
  () TO BE PUBLISHED --: --




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Organizational Affiliation: 

Department of Chemistry, University of Joensuu, Finland.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ASPARTYLGLUCOSAMINIDASE	A, C	162	Homo sapiens	Mutation(s): 0  Gene Names: AGA EC: 3.5.1.26
Find proteins for P20933 (Homo sapiens) Go to Gene View: AGA Go to UniProtKB:  P20933

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
ASPARTYLGLUCOSAMINIDASE	B, D	141	Homo sapiens	Mutation(s): 0  Gene Names: AGA EC: 3.5.1.26
Find proteins for P20933 (Homo sapiens) Go to Gene View: AGA Go to UniProtKB:  P20933

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
BMA	D	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NAG	A, B, C, D	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.224 
• R-Value Work: 0.169 
• Space Group: P 6₁

Unit Cell:

Length (Å)	Angle (°)
a = 98.400	α = 90.00
b = 98.400	β = 90.00
c = 134.500	γ = 120.00

Software Package:

Software Name	Purpose
X-PLOR	refinement
HKL	data collection
HKL	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-06-14 
• Released Date: 1996-12-23 
• Deposition Author(s): Rouvinen, J., Oinonen, C.

Revision History 

• Version 1.0: 1996-12-23
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance