PDBsum entry 3wso

Ligase

PDB id: 3wso

Contents

Protein chains

252 a.a.

139 a.a.

Waters ×16

PDB id:

3wso

Name:

Ligase

Title:

Crystal structure of the skp1-fbg3 complex

Structure:

F-box only protein 44. Chain: a. Synonym: f-box protein fbx30, f-box/g-domain protein 3. Engineered: yes. S-phase kinase-associated protein 1. Chain: b. Synonym: cyclin-a/cdk2-associated protein p19, organ of corti protein 2, ocp-2, organ of corti protein ii, ocp-ii, RNA polymerase ii elongation factor-like protein, siii, transcription elongation factor

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: fbxo44, fbg3, fbx30, fbx44, fbx6a, fbxo6a. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: skp1, emc19, ocp2, skp1a, tceb1l. Expression_system_taxid: 562

Resolution:

2.60Å R-factor: 0.208 R-free: 0.266

Authors:

T.Kumanomidou,K.Nishio,K.Takagi,T.Nakagawa,A.Suzuki,T.Yamane, F.Tokunaga,K.Iwai,A.Murakami,Y.Yoshida,K.Tanaka,T.Mizushima

Key ref:

T.Kumanomidou et al. (2015). The Structural Differences between a Glycoprotein Specific F-Box Protein Fbs1 and Its Homologous Protein FBG3. Plos One, 10, e0140366. PubMed id: 26460611 DOI: 10.1371/journal.pone.0140366

Date:

18-Mar-14 Release date: 25-Mar-15

Protein chain

Q9H4M3  (FBX44_HUMAN) -  F-box only protein 44 from Homo sapiens

Seq: 255 a.a.

Struc: 252 a.a.*

Protein chain

P63208  (SKP1_HUMAN) -  S-phase kinase-associated protein 1 from Homo sapiens

Seq: 163 a.a.

Struc: 139 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1371/journal.pone.0140366

Plos One 10:e0140366 (2015)

PubMed id: 26460611

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

T.Kumanomidou, K.Nishio, K.Takagi, T.Nakagawa, A.Suzuki, T.Yamane, F.Tokunaga, K.Iwai, A.Murakami, Y.Yoshida, K.Tanaka, T.Mizushima.

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.