8BS3

Structure of USP36 in complex with Fubi-PA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

Starting Models: in silico, experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Molecular basis for ubiquitin/Fubi cross-reactivity in USP16 and USP36.

O'Dea, R.Kazi, N.Hoffmann-Benito, A.Zhao, Z.Recknagel, S.Wendrich, K.Janning, P.Gersch, M.

(2023) Nat Chem Biol 19: 1394-1405

  • DOI: https://doi.org/10.1038/s41589-023-01388-1
  • Primary Citation of Related Structures:  
    8BS3, 8BS9

  • PubMed Abstract: 

    Ubiquitin and ubiquitin-like proteins typically use distinct machineries to facilitate diverse functions. The immunosuppressive ubiquitin-like protein Fubi is synthesized as an N-terminal fusion to a ribosomal protein (Fubi-S30). Its proteolytic maturation by the nucleolar deubiquitinase USP36 is strictly required for translationally competent ribosomes. What endows USP36 with this activity, how Fubi is recognized and whether other Fubi proteases exist are unclear. Here, we report a chemical tool kit that facilitated the discovery of dual ubiquitin/Fubi cleavage activity in USP16 in addition to USP36 by chemoproteomics. Crystal structures of USP36 complexed with Fubi and ubiquitin uncover its substrate recognition mechanism and explain how other deubiquitinases are restricted from Fubi. Furthermore, we introduce Fubi C-terminal hydrolase measurements and reveal a synergistic role of USP16 in Fubi-S30 maturation. Our data highlight how ubiquitin/Fubi specificity is achieved in a subset of human deubiquitinases and open the door to a systematic investigation of the Fubi system.


  • Organizational Affiliation

    Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Dortmund, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 36383Homo sapiensMutation(s): 0 
Gene Names: USP36KIAA1453
EC: 3.4.19.12 (PDB Primary Data), 2.3.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P275 (Homo sapiens)
Explore Q9P275 
Go to UniProtKB:  Q9P275
PHAROS:  Q9P275
GTEx:  ENSG00000055483 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P275
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3073Homo sapiensMutation(s): 0 
Gene Names: FAU
UniProt & NIH Common Fund Data Resources
Find proteins for P62861 (Homo sapiens)
Explore P62861 
Go to UniProtKB:  P62861
PHAROS:  P62861
GTEx:  ENSG00000149806 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62861
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.626α = 90
b = 75.892β = 90
c = 96.409γ = 90
Software Package:
Software NamePurpose
xia2data reduction
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermanyCGC-III-352S

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-07-26
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-15
    Changes: Database references