5KUT

hMiro2 C-terminal GTPase domain, GDP-bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural insights into Parkin substrate lysine targeting from minimal Miro substrates.

Klosowiak, J.L.Park, S.Smith, K.P.French, M.E.Focia, P.J.Freymann, D.M.Rice, S.E.

(2016) Sci Rep 6: 33019-33019

  • DOI: https://doi.org/10.1038/srep33019
  • Primary Citation of Related Structures:  
    5KSO, 5KSP, 5KSY, 5KSZ, 5KTY, 5KU1, 5KUT

  • PubMed Abstract: 

    Hereditary Parkinson's disease is commonly caused by mutations in the protein kinase PINK1 or the E3 ubiquitin ligase Parkin, which function together to eliminate damaged mitochondria. PINK1 phosphorylates both Parkin and ubiquitin to stimulate ubiquitination of dozens of proteins on the surface of the outer mitochondrial membrane. However, the mechanisms by which Parkin recognizes specific proteins for modification remain largely unexplored. Here, we show that the C-terminal GTPase (cGTPase) of the Parkin primary substrate human Miro is necessary and sufficient for efficient ubiquitination. We present several new X-ray crystal structures of both human Miro1 and Miro2 that reveal substrate recognition and ubiquitin transfer to be specific to particular protein domains and lysine residues. We also provide evidence that Parkin substrate recognition is functionally separate from substrate modification. Finally, we show that prioritization for modification of a specific lysine sidechain of the cGTPase (K572) within human Miro1 is dependent on both its location and chemical microenvironment. Activation of Parkin by phosphorylation or by binding of pUb is required for prioritization of K572 for modification, suggesting that Parkin activation and acquisition of substrate specificity are coupled.


  • Organizational Affiliation

    Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 90237, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial Rho GTPase 2
A, B, C
189Homo sapiensMutation(s): 1 
Gene Names: RHOT2ARHT2C16orf39
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IXI1 (Homo sapiens)
Explore Q8IXI1 
Go to UniProtKB:  Q8IXI1
GTEx:  ENSG00000140983 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IXI1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.61α = 90
b = 122.76β = 90
c = 103.89γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description