6DDA | pdb_00006dda

Nurr1 Covalently Modified by a Dopamine Metabolite

• PDB DOI: https://doi.org/10.2210/pdb6DDA/pdb

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


• Deposited: 2018-05-09 Released: 2019-03-20 
• Deposition Author(s): Bruning, J.M., Wang, Y., Otrabella, F., Boxue, T., Liu, H., Bhattacharya, P., Guo, S., Holton, J.M., Fletterick, R.J., Jacobson, M.P., England, P.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.294 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.252 (DCC) 

Literature

Covalent Modification and Regulation of the Nuclear Receptor Nurr1 by a Dopamine Metabolite.

Bruning, J.M., Wang, Y., Oltrabella, F., Tian, B., Kholodar, S.A., Liu, H., Bhattacharya, P., Guo, S., Holton, J.M., Fletterick, R.J., Jacobson, M.P., England, P.M.

(2019) Cell Chem Biol 26: 674-685.e6

• PubMed: 30853418 
• DOI: https://doi.org/10.1016/j.chembiol.2019.02.002
• Primary Citation Related Structures: 
  6DDA


• PubMed Abstract: 
  

  Nurr1, a nuclear receptor essential for the development, maintenance, and survival of midbrain dopaminergic neurons, is a potential therapeutic target for Parkinson's disease, a neurological disorder characterized by the degeneration of these same neurons. Efforts to identify Nurr1 agonists have been hampered by the recognition that it lacks several classic regulatory elements of nuclear receptor function, including the canonical ligand-binding pocket. Here we report that the dopamine metabolite 5,6-dihydroxyindole (DHI) binds directly to and modulates the activity of Nurr1. Using biophysical assays and X-ray crystallography, we show that DHI binds to the ligand-binding domain within a non-canonical pocket, forming a covalent adduct with Cys566. In cultured cells and zebrafish, DHI stimulates Nurr1 activity, including the transcription of target genes underlying dopamine homeostasis. These findings suggest avenues for developing synthetic Nurr1 ligands to ameliorate the symptoms and progression of Parkinson's disease.

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Organizational Affiliation: 
• Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA.
Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA.
Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA.
Bioengineering Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA.
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA.
Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA.
Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 93.24 kDa 
• Atom Count: 5,525 
• Modeled Residue Count: 685 
• Deposited Residue Count: 816 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor subfamily 4 group A member 2	A [auth B], C	272	Homo sapiens	Mutation(s): 0  Gene Names: NR4A2, NOT, NURR1, TINUR
UniProt & NIH Common Fund Data Resources
Find proteins for P43354 (Homo sapiens) Explore P43354  Go to UniProtKB:  P43354
PHAROS:  P43354 GTEx:  ENSG00000153234

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor subfamily 4 group A member 2	B [auth A]	272	Homo sapiens	Mutation(s): 0  Gene Names: NR4A2, NOT, NURR1, TINUR
UniProt & NIH Common Fund Data Resources
Find proteins for P43354 (Homo sapiens) Explore P43354  Go to UniProtKB:  P43354
PHAROS:  P43354 GTEx:  ENSG00000153234

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G7J	E [auth B], M [auth A], R [auth C]	5-hydroxy-1,2-dihydro-6H-indol-6-one C8 H7 N O2 RWEUJNADLANQCX-UHFFFAOYSA-N
BR	G [auth A], H [auth A], I [auth A], J [auth A], N [auth C], O [auth C], P [auth C]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
K	D [auth B], F [auth A], K [auth A], L [auth A], Q [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	B [auth A]	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.294 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.252 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.586	α = 90
b = 80.586	β = 90
c = 225.805	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-20 
Deposition Author(s): Bruning, J.M., Wang, Y., Otrabella, F., Boxue, T., Liu, H., Bhattacharya, P., Guo, S., Holton, J.M., Fletterick, R.J., Jacobson, M.P., England, P.M.

Revision History  

• Version 1.0: 2019-03-20
  Type: Initial release
  
• Version 1.1: 2019-05-01
  Changes: Data collection, Database references
• Version 1.2: 2019-05-29
  Changes: Data collection, Database references
• Version 1.3: 2019-11-06
  Changes: Author supporting evidence, Data collection
• Version 2.0: 2024-12-25
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary