7US1

Structure of parkin (R0RB) bound to two phospho-ubiquitin molecules


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

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Literature

Structure of the second phosphoubiquitin-binding site in parkin.

Fakih, R.Sauve, V.Gehring, K.

(2022) J Biol Chem 298: 102114-102114

  • DOI: 10.1016/j.jbc.2022.102114
  • Primary Citation of Related Structures:  
    7US1

  • PubMed Abstract: 
  • Parkin and PINK1 regulate a mitochondrial quality control system that is mutated in some early onset forms of Parkinson's disease. Parkin is an E3 ubiquitin ligase and regulated by the mitochondrial kinase PINK1 via a two-step cascade. PINK1 first phosphorylates ubiquitin, which binds a recruitment site on parkin to localize parkin to damaged mitochondria ...

    Parkin and PINK1 regulate a mitochondrial quality control system that is mutated in some early onset forms of Parkinson's disease. Parkin is an E3 ubiquitin ligase and regulated by the mitochondrial kinase PINK1 via a two-step cascade. PINK1 first phosphorylates ubiquitin, which binds a recruitment site on parkin to localize parkin to damaged mitochondria. In the second step, PINK1 phosphorylates parkin on its ubiquitin-like domain (Ubl) domain, which binds a regulatory site to release ubiquitin ligase activity. Recently, an alternative feed-forward mechanism was identified that bypasses the need for parkin phosphorylation through the binding of a second phospho-ubiquitin (pUb) molecule. Here, we report the structure of parkin activated through this feed-forward mechanism. The crystal structure of parkin with pUb bound to both the recruitment and regulatory sites reveals the molecular basis for differences in specificity and affinity of the two sites. We use isothermal titration calorimetry measurements to reveal cooperativity between the two binding sites and the role of linker residues for pUbl binding to the regulatory site. The observation of flexibility in the process of parkin activation offers hope for the future design of small molecules for the treatment of Parkinson's disease.


    Organizational Affiliation

    Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montreal, Quebec, Canada. Electronic address: kalle.gehring@mcgill.ca.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase parkinA240Rattus norvegicusMutation(s): 0 
Gene Names: Park2
EC: 2.3.2.31
UniProt
Find proteins for S4X0T1 (Rattus norvegicus)
Explore S4X0T1 
Go to UniProtKB:  S4X0T1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS4X0T1
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-G76 deletionB, C74Homo sapiensMutation(s): 0 
Gene Names: UBB
UniProt
Find proteins for J3QS39 (Homo sapiens)
Explore J3QS39 
Go to UniProtKB:  J3QS39
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ3QS39
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
B, C L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.078α = 90
b = 83.078β = 90
c = 253.816γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
PHENIXphasing
Cootmodel building
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Michael J. Fox FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release
  • Version 1.1: 2022-07-20
    Changes: Database references