6V88

Solution NMR structure of Dictyostelium discoideum Skp1A (truncated) dimer


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Skp1 Dimerization Conceals Its F-Box Protein Binding Site.

Kim, H.W.Eletsky, A.Gonzalez, K.J.van der Wel, H.Strauch, E.M.Prestegard, J.H.West, C.M.

(2020) Biochemistry 59: 1527-1536

  • DOI: 10.1021/acs.biochem.0c00094
  • Primary Citation of Related Structures:  
    6V88

  • PubMed Abstract: 
  • Skp1 is an adapter that links F-box proteins to cullin-1 in the Skp1/cullin-1/F-box (SCF) protein family of E3 ubiquitin ligases that targets specific proteins for polyubiquitination and subsequent protein degradation. Skp1 from the amoebozoan Dictyostelium forms a stable homodimer in vitro with a K d of 2 ...

    Skp1 is an adapter that links F-box proteins to cullin-1 in the Skp1/cullin-1/F-box (SCF) protein family of E3 ubiquitin ligases that targets specific proteins for polyubiquitination and subsequent protein degradation. Skp1 from the amoebozoan Dictyostelium forms a stable homodimer in vitro with a K d of 2.5 μM as determined by sedimentation velocity studies yet is monomeric in crystal complexes with F-box proteins. To investigate the molecular basis for the difference, we determined the solution NMR structure of a doubly truncated Skp1 homodimer (Skp1ΔΔ). The solution structure of the Skp1ΔΔ dimer reveals a 2-fold symmetry with an interface that buries ∼750 Å 2 of predominantly hydrophobic surface. The dimer interface overlaps with subsite 1 of the F-box interaction area, explaining why only the Skp1 monomer binds F-box proteins (FBPs). To confirm the model, Rosetta was used to predict amino acid substitutions that might disrupt the dimer interface, and the F97E substitution was chosen to potentially minimize interference with F-box interactions. A nearly full-length version of Skp1 with this substitution (Skp1ΔF97E) behaved as a stable monomer at concentrations of ≤500 μM and actively bound a model FBP, mammalian Fbs1, which suggests that the dimeric state is not required for Skp1 to carry out a basic biochemical function. Finally, Skp1ΔF97E is expected to serve as a monomer model for high-resolution NMR studies previously hindered by dimerization.


    Organizational Affiliation

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany. Electronic address: cmueller@embl.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SCF ubiquitin ligase complex protein SKP1aA, B116Dictyostelium discoideumMutation(s): 0 
Gene Names: fpaAfp21Afpa1fpa1Askp1ADDB_G0269230
Find proteins for P52285 (Dictyostelium discoideum)
Explore P52285 
Go to UniProtKB:  P52285
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 
  • OLDERADO: 6V88 Olderado

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesRO1GM037539
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM084383
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP41GM103390

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-15
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references