6BGL

Doubly PafE-capped 20S core particle in Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Proteasome substrate capture and gate opening by the accessory factor PafE fromMycobacterium tuberculosis.

Hu, K.Jastrab, J.B.Zhang, S.Kovach, A.Zhao, G.Darwin, K.H.Li, H.

(2018) J Biol Chem 293: 4713-4723

  • DOI: https://doi.org/10.1074/jbc.RA117.001471
  • Primary Citation of Related Structures:  
    6BGL, 6BGO

  • PubMed Abstract: 

    In all domains of life, proteasomes are gated, chambered proteases that require opening by activators to facilitate protein degradation. Twelve proteasome accessory factor E (PafE) monomers assemble into a single dodecameric ring that promotes proteolysis required for the full virulence of the human bacterial pathogen Mycobacterium tuberculosis Whereas the best characterized proteasome activators use ATP to deliver proteins into a proteasome, PafE does not require ATP. Here, to unravel the mechanism of PafE-mediated protein targeting and proteasome activation, we studied the interactions of PafE with native substrates, including a newly identified proteasome substrate, the ParA-like protein, Rv3213c, and with proteasome core particles. We characterized the function of a highly conserved feature in bacterial proteasome activator proteins: a glycine-glutamine-tyrosine-leucine (GQYL) motif at their C termini that is essential for stimulating proteolysis. Using cryo-electron microscopy (cryo-EM), we found that the GQYL motif of PafE interacts with specific residues in the α subunits of the proteasome core particle to trigger gate opening and degradation. Finally, we also found that PafE rings have 40-Å openings lined with hydrophobic residues that form a chamber for capturing substrates before they are degraded, suggesting PafE has a previously unrecognized chaperone activity. In summary, we have identified the interactions between PafE and the proteasome core particle that cause conformational changes leading to the opening of the proteasome gate and have uncovered a mechanism of PafE-mediated substrate degradation. Collectively, our results provide detailed insights into the mechanism of ATP-independent proteasome degradation in bacteria.


  • Organizational Affiliation

    Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, Michigan 49503.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha
A, C, D, E, F
A, C, D, E, F, G, H, I, J, K, L, M, N, O
248Mycobacterium tuberculosisMutation(s): 0 
Gene Names: prcAMRA_2124
EC: 3.4.25.1
UniProt
Find proteins for P9WHU1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHU1 
Go to UniProtKB:  P9WHU1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WHU1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Bacterial proteasome activator174Mycobacterium tuberculosisMutation(s): 0 
Gene Names: bpaMT3889
UniProt
Find proteins for P9WKX3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WKX3 
Go to UniProtKB:  P9WKX3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WKX3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta240Mycobacterium tuberculosisMutation(s): 0 
Gene Names: prcBMRA_2125
EC: 3.4.25.1
UniProt
Find proteins for P9WHT9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHT9 
Go to UniProtKB:  P9WHT9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WHT9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2018-02-14 
  • Deposition Author(s): Li, H., Hu, K.

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references
  • Version 1.2: 2018-04-11
    Changes: Data collection, Database references
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references