6E5Z

Crystal structure of human DJ-1 with a natural modification on Cys-106


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.112 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A transient post-translational modification of active site cysteine alters binding properties of the parkinsonism protein DJ-1.

Mussakhmetov, A.Shumilin, I.A.Nugmanova, R.Shabalin, I.G.Baizhumanov, T.Toibazar, D.Khassenov, B.Minor, W.Utepbergenov, D.

(2018) Biochem. Biophys. Res. Commun. 504: 328-333

  • DOI: 10.1016/j.bbrc.2018.08.190
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mutations in the human protein DJ-1 cause early onset of Parkinson's disease. A reactive cysteine residue (Cys <sup>106 </sup>) of DJ-1 is crucial for its protective function, although the underlying mechanisms are unclear. Here we show that a fracti ...

    Mutations in the human protein DJ-1 cause early onset of Parkinson's disease. A reactive cysteine residue (Cys 106 ) of DJ-1 is crucial for its protective function, although the underlying mechanisms are unclear. Here we show that a fraction of bacterially expressed polyhistidine-tagged human DJ-1 could not be eluted from a Ni-nitrilotriacetate (Ni-NTA) column with 150 mM imidazole. This unusually tight binding was accompanied by the appearance of blue violet color on the Ni-NTA column. We demonstrate by X-ray crystallography that Cys 106 is carboxymethylated in a fraction of DJ-1 tightly bound to Ni-NTA and that the replacement of Cys 106 by serine abrogates the tight binding and the appearance of blue violet color. However, carboxymethylation of purified DJ-1 is insufficient to confer the tight binding to Ni-NTA. Moreover, when eluted protein was re-applied to the Ni-NTA column, no tight binding was observed, indicating that the formation of high affinity complex with Ni-NTA depends on a transient modification of Cys 106 that transforms into a Cys 106 -carboxymethyl adduct upon elution from Ni-NTA. We conclude that an unknown metabolite reacts with Cys 106 of DJ-1 to result in a transient post-translational modification. This modification is distinct from simple oxidation to sulfinic or sulfenic acids and confers altered binding properties to DJ-1 suggesting that it could serve as a signal for sensing oxidant stress.


    Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22908, USA.,National Center for Biotechnology, Astana, 010000, Kazakhstan.,National Center for Biotechnology, Astana, 010000, Kazakhstan; Department of Chemistry, School of Science and Technology, Nazarbayev University, Astana, 010000, Kazakhstan.,Department of Biology, School of Science and Technology, Nazarbayev University, Astana, 010000, Kazakhstan.,Department of Chemistry, School of Science and Technology, Nazarbayev University, Astana, 010000, Kazakhstan. Electronic address: darkhan.utepbergenov@nu.edu.kz.,Department of Chemistry, School of Science and Technology, Nazarbayev University, Astana, 010000, Kazakhstan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein/nucleic acid deglycase DJ-1
A
191Homo sapiensMutation(s): 0 
Gene Names: PARK7
EC: 3.1.2.-, 3.5.1.-, 3.5.1.124
Find proteins for Q99497 (Homo sapiens)
Go to Gene View: PARK7
Go to UniProtKB:  Q99497
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CCS
Query on CCS
A
L-PEPTIDE LINKINGC5 H9 N O4 SCYS
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 74.715α = 90.00
b = 74.715β = 90.00
c = 74.807γ = 120.00
Software Package:
Software NamePurpose
HKL-3000data scaling
MOLREPphasing
REFMACrefinement
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited States--

Revision History 

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-10-10
    Type: Data collection, Database references, Structure summary
  • Version 1.2: 2019-04-17
    Type: Author supporting evidence, Data collection, Structure summary