7KPI

Crystal structure of the SPOP MATH domain

  • Classification: GENE REGULATION
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2020-11-11 Released: 2021-04-28 
  • Deposition Author(s): Usher, E.T., Boal, A.K.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Intrinsically disordered substrates dictate SPOP subnuclear localization and ubiquitination activity.

Usher, E.T.Sabri, N.Rohac, R.Boal, A.K.Mittag, T.Showalter, S.A.

(2021) J Biol Chem : 100693-100693

  • DOI: 10.1016/j.jbc.2021.100693
  • Primary Citation of Related Structures:  
    7KPK, 7KPI

  • PubMed Abstract: 
  • Speckle-type POZ protein (SPOP) is a ubiquitin ligase adaptor that binds substrate proteins and facilitates their proteasomal degradation. Most SPOP substrates present multiple SPOP-binding motifs and undergo liquid-liquid phase separation with SPOP. Pancreatic and duodenal homeobox 1 (Pdx1), an insulin transcription factor, is downregulated by interaction with SPOP ...

    Speckle-type POZ protein (SPOP) is a ubiquitin ligase adaptor that binds substrate proteins and facilitates their proteasomal degradation. Most SPOP substrates present multiple SPOP-binding motifs and undergo liquid-liquid phase separation with SPOP. Pancreatic and duodenal homeobox 1 (Pdx1), an insulin transcription factor, is downregulated by interaction with SPOP. Unlike other substrates, however, Pdx1 was reported to have just one SPOP-binding (SB) motif within its C-terminal disordered region (Pdx1-C). Given this difference, we aimed to determine the specific mode of interaction of Pdx1 with SPOP and how it is similar or different to that of other SPOP substrates. Here, we identify a second SPOP-binding motif in Pdx1-C, but still find that the resulting moderate valency is insufficient to support phase separation with SPOP in cells. While Pdx1 does not phase separate with SPOP, Pdx1 and SPOP interaction prompts SPOP re-localization from nuclear speckles to the diffuse nucleoplasm. Accordingly, we find that SPOP-mediated ubiquitination activity of Pdx1 occurs in the nucleoplasm and that highly efficient Pdx1 turnover requires both SB motifs. Our results suggest that the subnuclear localization of SPOP-substrate interactions and substrate ubiquitination may be directed by the properties of the substrate itself.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802; Department of Chemistry, Pennsylvania State University, University Park, PA 16802. Electronic address: sas76@psu.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Speckle-type POZ proteinA142Homo sapiensMutation(s): 0 
Gene Names: SPOP
UniProt & NIH Common Fund Data Resources
Find proteins for D6RDG8 (Homo sapiens)
Explore D6RDG8 
Go to UniProtKB:  D6RDG8
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.642α = 90
b = 53.246β = 101.386
c = 41.596γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01DK121509
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesF31DK124047

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    Type: Initial release
  • Version 1.1: 2021-05-05
    Changes: Database references