Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 20.17 kDa 
• Atom Count: 1615 
• Residue Count: 187 
• Unique protein chains: 1

6E5Z

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

• DOI: 10.2210/pdb6E5Z/pdb

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


• Deposited: 2018-07-23 Released: 2018-08-01 
• Deposition Author(s): Shumilin, I.A., Shumilina, S.V., Minor, W.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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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 

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:  
  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 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.

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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)
Find proteins for Q99497 (Homo sapiens) Explore Q99497  Go to UniProtKB:  Q99497
NIH Common Fund Data Resources
PHAROS:  Q99497 GTEx:  ENSG00000116288

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CCS	A	L-PEPTIDE LINKING	C5 H9 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.139 
• R-Value Work: 0.112 
• R-Value Observed: 0.113 
• Space Group: P 3₁ 2 1
• Diffraction Data DOI: 10.18430/m36e5z Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.715	α = 90
b = 74.715	β = 90
c = 74.807	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-07-23 
• Released Date: 2018-08-01 
Deposition Author(s): Shumilin, I.A., Shumilina, S.V., Minor, W.

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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: 2018-08-01
  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