Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 20.32 kDa 
• Atom Count: 1569 
• Modelled Residue Count: 187 
• Deposited Residue Count: 191 
• Unique protein chains: 1

6M8Z

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

• PDB DOI: 10.2210/pdb6M8Z/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-08-22 Released: 2018-09-05 
• Deposition Author(s): Shumilin, I.A., Shabalin, I.G., Shumilina, S.V., Werenskjold, C., Utepbergenov, D., Minor, W.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

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 

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

• PubMed: 30190129 
• 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. 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: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein/nucleic acid deglycase DJ-1	A	191	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	B [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.204 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 6₅ 2 2
• Diffraction Data DOI: 10.18430/m36m8z Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.5	α = 90
b = 66.5	β = 90
c = 176.728	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-08-22 
• Released Date: 2018-09-05 
Deposition Author(s): Shumilin, I.A., Shabalin, I.G., Shumilina, S.V., Werenskjold, C., Utepbergenov, D., Minor, W.

---

Funding Organization	Location	Grant 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
• Version 1.4: 2022-04-13
  Changes: Database references, Structure summary