PLoS ONE (Jan 2015)

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

  • Taichi Kumanomidou,
  • Kazuya Nishio,
  • Kenji Takagi,
  • Tomomi Nakagawa,
  • Atsuo Suzuki,
  • Takashi Yamane,
  • Fuminori Tokunaga,
  • Kazuhiro Iwai,
  • Arisa Murakami,
  • Yukiko Yoshida,
  • Keiji Tanaka,
  • Tsunehiro Mizushima

DOI
https://doi.org/10.1371/journal.pone.0140366
Journal volume & issue
Vol. 10, no. 10
p. e0140366

Abstract

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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.