3WSO

Crystal structure of the Skp1-FBG3 complex

Summary for 3WSO

• Entry DOI: 10.2210/pdb3wso/pdb
• Related: 2E31
• Descriptor: F-box only protein 44, S-phase kinase-associated protein 1 (3 entities in total)
• Functional Keywords: f-box protein, scf ubiquitin ligase, skp1, ligase
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 2
• Total formula weight: 48853.12

Authors

Kumanomidou, T.,Nishio, K.,Takagi, K.,Nakagawa, T.,Suzuki, A.,Yamane, T.,Tokunaga, F.,Iwai, K.,Murakami, A.,Yoshida, Y.,Tanaka, K.,Mizushima, T. (deposition date: 2014-03-18, release date: 2015-03-25, Last modification date: 2023-11-08)

Primary citation

Kumanomidou, T.,Nishio, K.,Takagi, K.,Nakagawa, T.,Suzuki, A.,Yamane, T.,Tokunaga, F.,Iwai, K.,Murakami, A.,Yoshida, Y.,Tanaka, K.,Mizushima, T.
The Structural Differences between a Glycoprotein Specific F-Box Protein Fbs1 and Its Homologous Protein FBG3
Plos One, 10:e0140366-e0140366, 2015

PubMed Abstract: The Skp1-Cul1-F-box protein (SCF) complex catalyzes protein ubiquitination in diverse cellular processes and is one of the best-characterized ubiquitin ligases. F-box proteins determine the substrate specificities of SCF ubiquitin ligases. Among these, Fbs1/FBG1/FBXO2, Fbs2/FBG2/FBXO6, and Fbs3/FBG5/FBXO27 recognize the N-glycans of glycoproteins, whereas FBG3/FBXO44 has no sugar-binding activity, despite the high sequence homology and conservation of the residues necessary for oligosaccharide binding between Fbs1-3 and FBG3. Here we determined the crystal structure of the Skp1-FBG3 complex at a resolution of 2.6 Å. The substrate-binding domain of FBG3 is composed of a 10-stranded antiparallel β-sandwich with three helices. Although the overall structure of FBG3 is similar to that of Fbs1, the residues that form the Fbs1 carbohydrate-binding pocket failed to be superposed with the corresponding residues of FBG3. Structure-based mutational analysis shows that distinct hydrogen bond networks of four FBG3 loops, i.e., β2-β3, β5-β6, β7-β8, and β9-β10, prevent the formation of the carbohydrate-binding pocket shown in Fbs1.

PubMed: 26460611
DOI: 10.1371/journal.pone.0140366

Experimental method

X-RAY DIFFRACTION (2.6 Å)