1APZ

HUMAN ASPARTYLGLUCOSAMINIDASE COMPLEX WITH REACTION PRODUCT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.Mol.Biol. 2: 1102-1108

  • Primary Citation of Related Structures:  1APY
  • Also Cited By: 1SEO, 2ZAL

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ASPARTYLGLUCOSAMINIDASE
A, C
162Homo sapiensGene 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
MoleculeChainsSequence LengthOrganismDetails
ASPARTYLGLUCOSAMINIDASE
B, D
141Homo sapiensGene 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

Download SDF File 
Download CCD File 
D
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ASP
Query on ASP

Download SDF File 
Download 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: 2.3 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.212 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 98.400α = 90.00
b = 98.400β = 90.00
c = 134.200γ = 120.00
Software Package:
Software NamePurpose
HKLdata collection
HKLdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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