8W31 | pdb_00008w31

Crystal structure of parkin (R0RB):2pUb with activator compound

• PDB DOI: https://doi.org/10.2210/pdb8W31/pdb

• Classification: LIGASE
• Organism(s): Rattus norvegicus, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-02-21 Released: 2024-08-21 
• Deposition Author(s): Sauve, V., Gehring, K.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.294 (Depositor), 0.294 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

Literature

Activation of parkin by a molecular glue.

Sauve, V., Stefan, E., Croteau, N., Goiran, T., Fakih, R., Bansal, N., Hadzipasic, A., Fang, J., Murugan, P., Chen, S., Fon, E.A., Hirst, W.D., Silvian, L.F., Trempe, J.F., Gehring, K.

(2024) Nat Commun 15: 7707-7707

• PubMed: 39300082 
• DOI: https://doi.org/10.1038/s41467-024-51889-3
• Primary Citation Related Structures: 
  8W31


• PubMed Abstract: 
  

  Mutations in parkin and PINK1 cause early-onset Parkinson's disease (EOPD). The ubiquitin ligase parkin is recruited to damaged mitochondria and activated by PINK1, a kinase that phosphorylates ubiquitin and the ubiquitin-like domain of parkin. Activated phospho-parkin then ubiquitinates mitochondrial proteins to target the damaged organelle for degradation. Here, we present the mechanism of activation of a new class of small molecule allosteric modulators that enhance parkin activity. The compounds act as molecular glues to enhance the ability of phospho-ubiquitin (pUb) to activate parkin. Ubiquitination assays and isothermal titration calorimetry with the most active compound (BIO-2007817) identify the mechanism of action. We present the crystal structure of a closely related compound (BIO-1975900) bound to a complex of parkin and two pUb molecules. The compound binds next to pUb on RING0 and contacts both proteins. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) experiments confirm that activation occurs through release of the catalytic Rcat domain. In organello and mitophagy assays demonstrate that BIO-2007817 partially rescues the activity of parkin EOPD mutants, R42P and V56E, offering a basis for the design of activators as therapeutics for Parkinson's disease.

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Organizational Affiliation: 
• Department of Biochemistry, McGill University, Montreal, QC, Canada.
Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada.
Biotherapeutics and Medicinal Sciences, Biogen, Cambridge, MA, USA.
Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada.
Structural Genomics Consortium, McGill University, Montreal, QC, Canada.
Brain Repair and Integrative Neuroscience (BRaIN) Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, QC, Canada.
Novartis Institutes for Biomedical Research, Cambridge, MA, USA.
Aura Biosciences, Boston, MA, USA.
Bristol-Myers Squibb, New York, NY, USA.
Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA, USA.
Neurodegenerative Disease Research Unit, Biogen, Cambridge, MA, USA.
DaCapo Brainscience, North Cambridge, MA, USA.
Biotherapeutics and Medicinal Sciences, Biogen, Cambridge, MA, USA. [e-mail].
Department of Biochemistry, McGill University, Montreal, QC, Canada. [e-mail].
Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 44.58 kDa 
• Atom Count: 3,051 
• Modeled Residue Count: 380 
• Deposited Residue Count: 390 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase parkin	A	240	Rattus norvegicus	Mutation(s): 0  Gene Names: Prkn, Park2 EC: 2.3.2.31
UniProt
Find proteins for Q9JK66 (Rattus norvegicus) Explore Q9JK66  Go to UniProtKB:  Q9JK66

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B, C	75	Homo sapiens	Mutation(s): 0  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AE9 (Subject of Investigation/LOI)	J [auth A]	(S)-1-(6-benzyl-3-(4-(1,2,3,4-tetrahydroquinoline-1-carbonyl)phenyl)-6,7-dihydropyrazolo[1,5-a]pyrazin-5(4H)-yl)ethan-1-one C31 H30 N4 O2 ZYSMPORNWLASGT-MHZLTWQESA-N
GOL	K [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	B, C	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.294 (Depositor), 0.294 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.54	α = 90
b = 83.54	β = 90
c = 258.77	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHENIX	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-08-21 
Deposition Author(s): Sauve, V., Gehring, K.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	FDN 159903

Revision History  

• Version 1.0: 2024-08-21
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Database references, Structure summary