7T9X

Saccharomyces cerevisiae Pex12 RING domain

  • Classification: LIGASE
  • Organism(s): Bacteria
  • Expression System: Bacteria
  • Mutation(s): No 

  • Deposited: 2021-12-20 Released: 2022-06-29 
  • Deposition Author(s): Feng, P., Rapoport, T.
  • Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A peroxisomal ubiquitin ligase complex forms a retrotranslocation channel.

Feng, P.Wu, X.Erramilli, S.K.Paulo, J.A.Knejski, P.Gygi, S.P.Kossiakoff, A.A.Rapoport, T.A.

(2022) Nature 607: 374-380

  • DOI: https://doi.org/10.1038/s41586-022-04903-x
  • Primary Citation of Related Structures:  
    7T92, 7T9X

  • PubMed Abstract: 

    Peroxisomes are ubiquitous organelles that house various metabolic reactions and are essential for human health 1-4 . Luminal peroxisomal proteins are imported from the cytosol by mobile receptors, which then recycle back to the cytosol by a poorly understood process 1-4 . Recycling requires receptor modification by a membrane-embedded ubiquitin ligase complex comprising three RING finger domain-containing proteins (Pex2, Pex10 and Pex12) 5,6 . Here we report a cryo-electron microscopy structure of the ligase complex, which together with biochemical and in vivo experiments reveals its function as a retrotranslocation channel for peroxisomal import receptors. Each subunit of the complex contributes five transmembrane segments that co-assemble into an open channel. The three ring finger domains form a cytosolic tower, with ring finger 2 (RF2) positioned above the channel pore. We propose that the N terminus of a recycling receptor is inserted from the peroxisomal lumen into the pore and monoubiquitylated by RF2 to enable extraction into the cytosol. If recycling is compromised, receptors are polyubiquitylated by the concerted action of RF10 and RF12 and degraded. This polyubiquitylation pathway also maintains the homeostasis of other peroxisomal import factors. Our results clarify a crucial step during peroxisomal protein import and reveal why mutations in the ligase complex cause human disease.


  • Organizational Affiliation

    Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. peiqiang_feng@hms.harvard.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome assembly protein 12
A, B
73BacteriaMutation(s): 0 
Gene Names: PEX12YMR026CYM9711.16C
UniProt
Find proteins for Q04370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04370 
Go to UniProtKB:  Q04370
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04370
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.578α = 90
b = 32.922β = 100.715
c = 72.488γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-29
    Type: Initial release
  • Version 1.1: 2022-07-13
    Changes: Database references
  • Version 1.2: 2022-07-20
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Refinement description