4P35

Crystal structure of DJ-1 with Zinc(II) bound (crystal I)

• PDB DOI: https://doi.org/10.2210/pdb4P35/pdb

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


• Deposited: 2014-03-05 Released: 2014-04-09 
• Deposition Author(s): Tashiro, S., Wu, C.-X., Hoang, Q.Q., Caaveiro, J.M.M., Tsumoto, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.171 
• R-Value Work: 0.142 
• R-Value Observed: 0.143 

Literature

Thermodynamic and Structural Characterization of the Specific Binding of Zn(II) to Human Protein DJ-1.

Tashiro, S., Caaveiro, J.M., Wu, C.X., Hoang, Q.Q., Tsumoto, K.

(2014) Biochemistry 53: 2218-2220

• PubMed: 24697266 
• DOI: https://doi.org/10.1021/bi500294h
• Primary Citation of Related Structures:  
  4P2G, 4P34, 4P35, 4P36


• PubMed Abstract: 
  

  Mutations of DJ-1 cause familial Parkinson's disease (PD), although the role of DJ-1 in PD remains unresolved. Very recent reports have shown that DJ-1 interacts with copper ions. This evidence opens new avenues to understanding the function of DJ-1 and its role in PD. Herein, we report that Zn(II) binds to DJ-1 with great selectivity among the other metals examined: Mn(II), Fe(II), Co(II), Ni(II), and Cu(II). High-resolution X-ray crystallography (1.18 Å resolution) shows Zn(II) is coordinated to the protein by the key residues Cys106 and Glu18. These results suggest that DJ-1 may be regulated and/or stabilized by Zn(II).

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Organizational Affiliation: 

Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo , Kashiwa 277-8562, Japan.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 20.11 kDa 
• Atom Count: 1,631 
• Modelled Residue Count: 187 
• Deposited Residue Count: 189 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein DJ-1	A	189	Homo sapiens	Mutation(s): 0  Gene Names: PARK7 EC: 3.4
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.171 
• R-Value Work: 0.142 
• R-Value Observed: 0.143 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.13	α = 90
b = 75.13	β = 90
c = 75.54	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-09 
Deposition Author(s): Tashiro, S., Wu, C.-X., Hoang, Q.Q., Caaveiro, J.M.M., Tsumoto, K.

Revision History  

• Version 1.0: 2014-04-09
  Type: Initial release
  
• Version 1.1: 2014-05-14
  Changes: Database references
• Version 1.2: 2014-07-23
  Changes: Structure summary
• Version 1.3: 2015-09-23
  Changes: Other
• Version 1.4: 2017-11-22
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.5: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description