3B3A | pdb_00003b3a

Structure of E163K/R145E DJ-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.203 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural Impact of Three Parkinsonism-Associated Missense Mutations on Human DJ-1.

Lakshminarasimhan, M.Maldonado, M.T.Zhou, W.Fink, A.L.Wilson, M.A.

(2008) Biochemistry 47: 1381-1392

  • DOI: https://doi.org/10.1021/bi701189c
  • Primary Citation Related Structures: 
    2RK3, 2RK4, 2RK6, 3B36, 3B38, 3B3A

  • PubMed Abstract: 

    A number of missense mutations in the oxidative stress response protein DJ-1 are implicated in rare forms of familial Parkinsonism. The best-characterized Parkinsonian DJ-1 missense mutation, L166P, disrupts homodimerization and results in a poorly folded protein. The molecular basis by which the other Parkinsonism-associated mutations disrupt the function of DJ-1, however, is incompletely understood. In this study we show that three different Parkinsonism-associated DJ-1 missense mutations (A104T, E163K, and M26I) reduce the thermal stability of DJ-1 in solution by subtly perturbing the structure of DJ-1 without causing major folding defects or loss of dimerization. Atomic resolution X-ray crystallography shows that the A104T substitution introduces water and a discretely disordered residue into the core of the protein, E163K disrupts a key salt bridge with R145, and M26I causes packing defects in the core of the dimer. The deleterious effect of each Parkinsonism-associated mutation on DJ-1 is dissected by analysis of engineered substitutions (M26L, A104V, and E163K/R145E) that partially alleviate each of the defects introduced by the A104T, E163K and M26I mutations. In total, our results suggest that the protective function of DJ-1 can be compromised by diverse perturbations in its structural integrity, particularly near the junctions of secondary structural elements.


  • Organizational Affiliation
    • Department of Biochemistry and the Redox Biology Center, The University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0664, USA.

Macromolecule Content 

  • Total Structure Weight: 20.39 kDa 
  • Atom Count: 1,630 
  • Modeled Residue Count: 187 
  • Deposited Residue Count: 192 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein DJ-1192Homo sapiensMutation(s): 2 
Gene Names: PARK7
EC: 3.5.1 (UniProt), 3.1.2 (UniProt), 3.5.1.124 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q99497 (Homo sapiens)
Explore Q99497 
Go to UniProtKB:  Q99497
PHAROS:  Q99497
GTEx:  ENSG00000116288 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99497
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.203 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.987α = 90
b = 74.987β = 90
c = 75.11γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-08-30
    Changes: Data collection, Refinement description