5TR5

Solution structure of Serine 65 phosphorylated UBL domain from parkin


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 25 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of phosphorylated UBL domain and insights into PINK1-orchestrated parkin activation.

Aguirre, J.D.Dunkerley, K.M.Mercier, P.Shaw, G.S.

(2017) Proc Natl Acad Sci U S A 114: 298-303

  • DOI: 10.1073/pnas.1613040114
  • Primary Citation of Related Structures:  
    5TR5

  • PubMed Abstract: 
  • Mutations in PARK2 and PARK6 genes are responsible for the majority of hereditary Parkinson's disease cases. These genes encode the E3 ubiquitin ligase parkin and the protein kinase PTEN-induced kinase 1 (PINK1), respectively. Together, parkin and PI ...

    Mutations in PARK2 and PARK6 genes are responsible for the majority of hereditary Parkinson's disease cases. These genes encode the E3 ubiquitin ligase parkin and the protein kinase PTEN-induced kinase 1 (PINK1), respectively. Together, parkin and PINK1 regulate the mitophagy pathway, which recycles damaged mitochondria following oxidative stress. Native parkin is inactive and exists in an autoinhibited state mediated by its ubiquitin-like (UBL) domain. PINK1 phosphorylation of serine 65 in parkin's UBL and serine 65 of ubiquitin fully activate ubiquitin ligase activity; however, a structural rationale for these observations is not clear. Here, we report the structure of the phosphorylated UBL domain from parkin. We find that destabilization of the UBL results from rearrangements to hydrophobic core packing that modify its structure. Altered surface electrostatics from the phosphoserine group disrupt its intramolecular association, resulting in poorer autoinhibition in phosphorylated parkin. Further, we show that phosphorylation of both the UBL domain and ubiquitin are required to activate parkin by releasing the UBL domain, forming an extended structure needed to facilitate E2-ubiquitin binding. Together, the results underscore the importance of parkin activation by the PINK1 phosphorylation signal and provide a structural picture of the unraveling of parkin's ubiquitin ligase potential.


    Organizational Affiliation

    Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON N6A 3K7, Canada gshaw1@uwo.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase parkinA76Homo sapiensMutation(s): 0 
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
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 25 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 5TR5 Olderado

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP-14606

Revision History 

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2017-01-04
    Changes: Database references
  • Version 1.2: 2017-01-25
    Changes: Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence, Structure summary