1APZ

HUMAN ASPARTYLGLUCOSAMINIDASE COMPLEX WITH REACTION PRODUCT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

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: 10.1038/nsb1295-1102
  • Primary Citation of Related Structures:  
    1APZ, 1APY

  • 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 ...

    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.


    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 --: --

    Organizational Affiliation

    Department of Chemistry, University of Joensuu, Finland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ASPARTYLGLUCOSAMINIDASE AC162Homo sapiensMutation(s): 0 
Gene Names: AGA
EC: 3.5.1.26
Find proteins for P20933 (Homo sapiens)
Explore P20933 
Go to UniProtKB:  P20933
NIH Common Fund Data Resources
PHAROS:  P20933
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ASPARTYLGLUCOSAMINIDASE BD141Homo sapiensMutation(s): 0 
Gene Names: AGA
EC: 3.5.1.26
Find proteins for P20933 (Homo sapiens)
Explore P20933 
Go to UniProtKB:  P20933
NIH Common Fund Data Resources
PHAROS:  P20933
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain 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
3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A, B, C
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ASP
Query on ASP

Download Ideal Coordinates CCD File 
B, D
ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.4α = 90
b = 98.4β = 90
c = 134.2γ = 120
Software Package:
Software NamePurpose
HKLdata collection
X-PLORrefinement
HKLdata reduction

Structure Validation

View Full Validation Report



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