6DEY

Aspartylglucosaminuria mutant structure and function


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Biochemical and structural insights into an allelic variant causing the lysosomal storage disorder - aspartylglucosaminuria.

Pande, S.Bizilj, W.Guo, H.C.

(2018) FEBS Lett 592: 2550-2561

  • DOI: https://doi.org/10.1002/1873-3468.13190
  • Primary Citation of Related Structures:  
    6DEY

  • PubMed Abstract: 

    Aspartylglucosaminuria (AGU) is a lysosomal storage disorder caused by defects of the hydrolase glycosylasparaginase (GA). Previously, we showed that a Canadian AGU mutation disrupts an obligatory intramolecular autoprocessing with the enzyme trapped as an inactive precursor. Here, we report biochemical and structural characterizations of a model enzyme corresponding to a Finnish AGU allele, the T234I variant. Unlike the Canadian counterpart, the Finnish variant is capable of a slow autoprocessing to generate detectible hydrolyzation activity of the natural substrate of GA. We have determined a 1.6 Å-resolution structure of the Finnish AGU model and built an enzyme-substrate complex to provide a structural basis for analyzing the negative effects of the point mutation on K M and k cat of the mature enzyme.


  • Organizational Affiliation

    Department of Biological Sciences, University of Massachusetts Lowell, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycosylasparaginase, residues 38-178
A, C
141Elizabethkingia meningosepticaMutation(s): 0 
Gene Names: BMF97_04835
UniProt
Find proteins for A0A1V3U2Z4 (Elizabethkingia meningoseptica)
Explore A0A1V3U2Z4 
Go to UniProtKB:  A0A1V3U2Z4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1V3U2Z4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glycosylasparaginase, residues 188-331
B, D
144Elizabethkingia meningosepticaMutation(s): 0 
Gene Names: BMF97_04835
UniProt
Find proteins for A0A1V3U2Z4 (Elizabethkingia meningoseptica)
Explore A0A1V3U2Z4 
Go to UniProtKB:  A0A1V3U2Z4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1V3U2Z4
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.98α = 90
b = 96.56β = 90.26
c = 61.75γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesDK075294

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-09-12
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references