6V88

Solution NMR structure of Dictyostelium discoideum Skp1A (truncated) dimer

Summary for 6V88

• Entry DOI: 10.2210/pdb6v88/pdb
• NMR Information: BMRB: 30696
• Descriptor: SCF ubiquitin ligase complex protein SKP1a (1 entity in total)
• Functional Keywords: ubiquitin ligase e3 scf complex skp1, protein binding
• Biological source: Dictyostelium discoideum (Slime mold); More
• Total number of polymer chains: 2
• Total formula weight: 25997.78

Authors

Kim, H.W.,Eletsky, A.,West, C.M. (deposition date: 2019-12-10, release date: 2020-04-15, Last modification date: 2024-05-15)

Primary citation

Kim, H.W.,Eletsky, A.,Gonzalez, K.J.,van der Wel, H.,Strauch, E.M.,Prestegard, J.H.,West, C.M.
Skp1 Dimerization Conceals Its F-Box Protein Binding Site.
Biochemistry, 59:1527-1536, 2020

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 forms a stable homodimer with a 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 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.

PubMed: 32227851
DOI: 10.1021/acs.biochem.0c00094

Experimental method

SOLUTION NMR