6AFB

DJ-1 C106S incubated with isatin

• PDB DOI:  https://doi.org/10.2210/pdb6AFB/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2018-08-08 Released: 2018-08-29 
• Deposition Author(s): Caaveiro, J.M.M., Tashiro, S., Tsumoto, K.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan), Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.172 
• R-Value Work: 0.145 
• R-Value Observed: 0.146 

Literature

Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.

Tashiro, S., Caaveiro, J.M.M., Nakakido, M., Tanabe, A., Nagatoishi, S., Tamura, Y., Matsuda, N., Liu, D., Hoang, Q.Q., Tsumoto, K.

(2018) ACS Chem Biol 13: 2783-2793

• PubMed: 30063823 
• DOI: https://doi.org/10.1021/acschembio.8b00701
• Primary Citation of Related Structures:  
  6AF5, 6AF7, 6AF9, 6AFA, 6AFB, 6AFC, 6AFD, 6AFE, 6AFF, 6AFG, 6AFH, 6AFI, 6AFJ, 6AFL


• PubMed Abstract: 
  

DJ-1 is a Parkinson's disease associated protein endowed with enzymatic, redox sensing, regulatory, chaperoning, and neuroprotective activities. Although DJ-1 has been vigorously studied for the past decade and a half, its exact role in the progression of the disease remains uncertain. In addition, little is known about the spatiotemporal regulation of DJ-1, or the biochemical basis explaining its numerous biological functions. Progress has been hampered by the lack of inhibitors with precisely known mechanisms of action. Herein, we have employed biophysical methodologies and X-ray crystallography to identify and to optimize a family of compounds inactivating the critical Cys106 residue of human DJ-1. We demonstrate these compounds are potent inhibitors of various activities of DJ-1 in vitro and in cell-based assays. This study reports a new family of DJ-1 inhibitors with a defined mechanism of action, and contributes toward the understanding of the biological function of DJ-1.

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Related Citations: 

• Thermodynamic and structural characterization of the specific binding of Zn(II) to human protein DJ-1.
  Tashiro, S., Caaveiro, J.M.M., Wu, C.X., Hoang, Q.Q., Tsumoto, K.
  (2014) Biochemistry 53: 2218

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Organizational Affiliation: 

Department of Chemistry and Biotechnology, School of Engineering , The University of Tokyo , Tokyo 108-8639 , Japan.

Biological Assembly 1  

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: 20.31 kDa 
• Atom Count: 1,662 
• Modelled Residue Count: 187 
• Deposited Residue Count: 189 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein/nucleic acid deglycase DJ-1	A	189	Homo sapiens	Mutation(s): 1  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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ISN	B [auth A], C [auth A]	ISATIN C8 H5 N O2 JXDYKVIHCLTXOP-UHFFFAOYSA-N
DMS	E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.172 
• R-Value Work: 0.145 
• R-Value Observed: 0.146 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.86	α = 90
b = 74.86	β = 90
c = 74.69	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-29 
Deposition Author(s): Caaveiro, J.M.M., Tashiro, S., Tsumoto, K.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	Platform for Drug Discovery, Informatics and Structural Life Science
Japan Society for the Promotion of Science	Japan	25249115
Japan Society for the Promotion of Science	Japan	16H02420
Japan Society for the Promotion of Science	Japan	15K06962

Revision History  

• Version 1.0: 2018-08-29
  Type: Initial release
  
• Version 1.1: 2018-10-03
  Changes: Data collection, Database references