The Structural Differences between a Glycoprotein Specific F-Box Protein Fbs1 and Its Homologous Protein FBG3

• Published in: PloS one 2015-10, Vol.10 (10), p.e0140366-e0140366
• Main Authors: Kumanomidou, Taichi, Nishio, Kazuya, Takagi, Kenji, Nakagawa, Tomomi, Suzuki, Atsuo, Yamane, Takashi, Tokunaga, Fuminori, Iwai, Kazuhiro, Murakami, Arisa, Yoshida, Yukiko, Tanaka, Keiji, Mizushima, Tsunehiro
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Analysis; Binding; Carbohydrates; Cascades (Fluid dynamics); Cell Cycle Proteins - chemistry; Conservation; Conserved sequence; Crystal structure; Crystallography, X-Ray; F-box protein; F-Box Proteins - chemistry; F-Box Proteins - genetics; Glycoproteins; Glycoproteins - metabolism; Helices; Homology; Humans; Hydrogen; Hydrogen bonds; Models, Molecular; Molecular Sequence Data; Mutant Proteins - metabolism; Mutation - genetics; N-glycans; Nerve Tissue Proteins - chemistry; Next-generation sequencing; Polysaccharides; Protein Binding; Protein Structure, Tertiary; Proteins; Residues; Ribonucleases - metabolism; S-Phase Kinase-Associated Proteins - chemistry; Sequence Homology, Amino Acid; Substrate Specificity; Substrates; Sugar; Ubiquitin; Ubiquitin-proteasome system; Ubiquitination
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0140366

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.