1APY

HUMAN ASPARTYLGLUCOSAMINIDASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Three-dimensional structure of human lysosomal aspartylglucosaminidase.

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

(1995) Nat Struct Biol 2: 1102-1108

  • DOI: https://doi.org/10.1038/nsb1295-1102
  • Primary Citation of Related Structures:  
    1APY, 1APZ

  • 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.


  • Organizational Affiliation

    Department of Chemistry, University of Joensuu, Finland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ASPARTYLGLUCOSAMINIDASE
A, C
162Homo sapiensMutation(s): 0 
EC: 3.5.1.26
UniProt & NIH Common Fund Data Resources
Find proteins for P20933 (Homo sapiens)
Explore P20933 
Go to UniProtKB:  P20933
PHAROS:  P20933
GTEx:  ENSG00000038002 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20933
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ASPARTYLGLUCOSAMINIDASE
B, D
141Homo sapiensMutation(s): 0 
EC: 3.5.1.26
UniProt & NIH Common Fund Data Resources
Find proteins for P20933 (Homo sapiens)
Explore P20933 
Go to UniProtKB:  P20933
PHAROS:  P20933
GTEx:  ENSG00000038002 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20933
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth B],
H [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.4α = 90
b = 98.4β = 90
c = 134.5γ = 120
Software Package:
Software NamePurpose
HKLdata collection
X-PLORrefinement
HKLdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-12-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary