title: The Structural Differences between a Glycoprotein Specific F-Box Protein Fbs1 and Its Homologous Protein FBG3.
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.
authors.affiliation: Department of Biotechnology, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, Japan.
authors.forename: Taichi
authors.initials: T
authors.lastname: Kumanomidou
authors.affiliation: Picobiology Institute, Department of Life Science, Graduate School of Life Science, University of Hyogo, Kouto, Kamigori-cho, Ako-gun, Hyogo, Japan.
authors.forename: Kazuya
authors.initials: K
authors.lastname: Nishio
authors.affiliation: Picobiology Institute, Department of Life Science, Graduate School of Life Science, University of Hyogo, Kouto, Kamigori-cho, Ako-gun, Hyogo, Japan.
authors.forename: Kenji
authors.initials: K
authors.lastname: Takagi
authors.affiliation: Department of Biotechnology, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, Japan.
authors.forename: Tomomi
authors.initials: T
authors.lastname: Nakagawa
authors.affiliation: Department of Biotechnology, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, Japan.
authors.forename: Atsuo
authors.initials: A
authors.lastname: Suzuki
authors.affiliation: Department of Biotechnology, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Yamane
authors.affiliation: Laboratory of Molecular Cell Biology, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan.
authors.forename: Fuminori
authors.initials: F
authors.lastname: Tokunaga
authors.affiliation: Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan.
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Iwai
authors.affiliation: Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo, Japan.
authors.forename: Arisa
authors.initials: A
authors.lastname: Murakami
authors.affiliation: Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo, Japan.
authors.forename: Yukiko
authors.initials: Y
authors.lastname: Yoshida
authors.affiliation: Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo, Japan.
authors.forename: Keiji
authors.initials: K
authors.lastname: Tanaka
authors.affiliation: Picobiology Institute, Department of Life Science, Graduate School of Life Science, University of Hyogo, Kouto, Kamigori-cho, Ako-gun, Hyogo, Japan.
authors.forename: Tsunehiro
authors.initials: T
authors.lastname: Mizushima
mesh_terms: D000595:Amino Acid Sequence; D018797:Cell Cycle Proteins / Q000737:chemistry*; D018360:Crystallography, X-Ray; D044783:F-Box Proteins / Q000737:chemistry* / Q000235:genetics; D006023:Glycoproteins / Q000378:metabolism*; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D050505:Mutant Proteins / Q000378:metabolism; D009154:Mutation / Q000235:genetics; D009419:Nerve Tissue Proteins / Q000737:chemistry*; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012260:Ribonucleases / Q000378:metabolism; D044786:S-Phase Kinase-Associated Proteins / Q000737:chemistry; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity
chemical_list: D018797:Cell Cycle Proteins; D044783:F-Box Proteins; C485508:FBXO2 protein, human; C578089:FBXO44 protein, human; D006023:Glycoproteins; D050505:Mutant Proteins; D009419:Nerve Tissue Proteins; D044786:S-Phase Kinase-Associated Proteins; C097351:SKP1 protein, human; D012260:Ribonucleases; C029600:ribonuclease B