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 
  • R-Value Observed: 0.113 

wwPDB Validation   3D Report Full Report


This is version 1.4 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:  
    6E5Z, 6M8Z

  • 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 of bacterially expressed polyhistidine-tagged human DJ-1 could not be eluted from a Ni-nitrilotriacetate (Ni-NTA) column with 150 mM imidazole ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein/nucleic acid deglycase DJ-1A191Homo 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)
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL
Download Ideal Coordinates CCD File 
B [auth A],
C [auth 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
b = 74.715β = 90
c = 74.807γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing

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  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-10-10
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2019-04-17
    Changes: Author supporting evidence, Data collection, Structure summary
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.4: 2022-04-13
    Changes: Database references, Structure summary