5C9V

Structure of human Parkin G319A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanism of phospho-ubiquitin-induced PARKIN activation.

Wauer, T.Simicek, M.Schubert, A.Komander, D.

(2015) Nature 524: 370-374

  • DOI: 10.1038/nature14879
  • Primary Citation of Related Structures:  
    5C9V, 5CAW

  • PubMed Abstract: 
  • The E3 ubiquitin ligase PARKIN (encoded by PARK2) and the protein kinase PINK1 (encoded by PARK6) are mutated in autosomal-recessive juvenile Parkinsonism (AR-JP) and work together in the disposal of damaged mitochondria by mitophagy. PINK1 is stabil ...

    The E3 ubiquitin ligase PARKIN (encoded by PARK2) and the protein kinase PINK1 (encoded by PARK6) are mutated in autosomal-recessive juvenile Parkinsonism (AR-JP) and work together in the disposal of damaged mitochondria by mitophagy. PINK1 is stabilized on the outside of depolarized mitochondria and phosphorylates polyubiquitin as well as the PARKIN ubiquitin-like (Ubl) domain. These phosphorylation events lead to PARKIN recruitment to mitochondria, and activation by an unknown allosteric mechanism. Here we present the crystal structure of Pediculus humanus PARKIN in complex with Ser65-phosphorylated ubiquitin (phosphoUb), revealing the molecular basis for PARKIN recruitment and activation. The phosphoUb binding site on PARKIN comprises a conserved phosphate pocket and harbours residues mutated in patients with AR-JP. PhosphoUb binding leads to straightening of a helix in the RING1 domain, and the resulting conformational changes release the Ubl domain from the PARKIN core; this activates PARKIN. Moreover, phosphoUb-mediated Ubl release enhances Ubl phosphorylation by PINK1, leading to conformational changes within the Ubl domain and stabilization of an open, active conformation of PARKIN. We redefine the role of the Ubl domain not only as an inhibitory but also as an activating element that is restrained in inactive PARKIN and released by phosphoUb. Our work opens up new avenues to identify small-molecule PARKIN activators.


    Related Citations: 
    • Structure of the human Parkin ligase domain in an autoinhibited state.
      Wauer, T., Komander, D.
      (2013) EMBO J 32: 2099

    Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase parkinA330Homo sapiensMutation(s): 1 
Gene Names: PARK2PRKN
EC: 6.3.2 (PDB Primary Data), 2.3.2.31 (UniProt)
Find proteins for O60260 (Homo sapiens)
Explore O60260 
Go to UniProtKB:  O60260
NIH Common Fund Data Resources
PHAROS  O60260
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.36α = 90
b = 169.36β = 90
c = 96.99γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomU105192732
European Research CouncilUnited Kingdom309756

Revision History 

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-07-29
    Changes: Database references
  • Version 1.2: 2015-08-26
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence