1P5F

Crystal Structure of Human DJ-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The 1.1 A resolution crystal structure of DJ-1, the protein mutated in autosomal recessive early onset Parkinson's disease

Wilson, M.A.Collins, J.L.Hod, Y.Ringe, D.Petsko, G.A.

(2003) Proc.Natl.Acad.Sci.USA 100: 9256-9261

  • DOI: 10.1073/pnas.1133288100

  • PubMed Abstract: 
  • Mutations in DJ-1, a human gene with homologues in organisms from all kingdoms of life, have been shown to be associated with autosomal recessive, early onset Parkinson's disease (PARK7). We report here the three-dimensional structure of the DJ-1 pro ...

    Mutations in DJ-1, a human gene with homologues in organisms from all kingdoms of life, have been shown to be associated with autosomal recessive, early onset Parkinson's disease (PARK7). We report here the three-dimensional structure of the DJ-1 protein, determined at a resolution of 1.1 A by x-ray crystallography. The chain fold of DJ-1 resembles those of a bacterial protein, PfpI, that has been annotated as a cysteine protease, and of a domain of a bacterial catalase whose role in the activity of that enzyme is uncertain. In contrast to PfpI, a hexameric protein whose oligomeric structure is essential for its putative proteolytic activity, DJ-1 is a dimer with completely different intersubunit contacts. The proposed catalytic triad of PfpI is absent from the corresponding region of the structure of DJ-1, and biochemical assays fail to detect any protease activity for purified DJ-1. A highly conserved cysteine residue, which is catalytically essential in homologues of DJ-1, shows an extreme sensitivity to radiation damage and may be subject to other forms of oxidative modification as well. The structure suggests that the loss of function caused by the Parkinson's-associated mutation L166P in DJ-1 is due to destabilization of the dimer interface. Taken together, the crystal structure of human DJ-1 plus other observations suggest the possible involvement of this protein in the cellular oxidative stress response and a general etiology of neurodegenerative diseases.


    Organizational Affiliation

    Department of Biochemistry and Chemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, 415 South Street, MS 029, Waltham, MA 02454-9110, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-binding protein regulatory subunit
A
189Homo sapiensGene Names: PARK7
EC: 3.1.2.-, 3.5.1.-
Find proteins for Q99497 (Homo sapiens)
Go to Gene View: PARK7
Go to UniProtKB:  Q99497
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.139 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 75.306α = 90.00
b = 75.306β = 90.00
c = 75.422γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SOLVEphasing
DENZOdata reduction
RESOLVEphasing
SHELXL-97refinement
SHELXmodel building
RESOLVEmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-12
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description
  • Version 1.4: 2018-01-31
    Type: Experimental preparation