6M8Z

Crystal structure of human DJ-1 without a modification on Cys-106


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    6M8Z, 6E5Z

  • PubMed Abstract: 
  • 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 o ...

    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 Chemistry, School of Science and Technology, Nazarbayev University, Astana, 010000, Kazakhstan. Electronic address: darkhan.utepbergenov@nu.edu.kz.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein/nucleic acid deglycase DJ-1 A191Homo sapiensMutation(s): 0 
Gene Names: PARK7
EC: 3.1.2 (PDB Primary Data), 3.5.1 (PDB Primary Data), 3.5.1.124 (PDB Primary Data)
Find proteins for Q99497 (Homo sapiens)
Explore Q99497 
Go to UniProtKB:  Q99497
NIH Common Fund Data Resources
PHAROS:  Q99497
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.5α = 90
b = 66.5β = 90
c = 176.728γ = 120
Software Package:
Software NamePurpose
HKL-3000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000phasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History 

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2018-09-19
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-17
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence