2E32

Structural basis for selection of glycosylated substrate by SCFFbs1 ubiquitin ligase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.52 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for the selection of glycosylated substrates by SCFFbs1 ubiquitin ligase

Mizushima, T.Yoshida, Y.Kumanomidou, T.Hasegawa, Y.Suzuki, A.Yamane, T.Tanaka, K.

(2007) Proc Natl Acad Sci U S A 104: 5777-5781

  • DOI: 10.1073/pnas.0610312104
  • Primary Citation of Related Structures:  
    2E33, 2E32, 2E31

  • PubMed Abstract: 
  • The ubiquitin ligase complex SCF(Fbs1), which contributes to the ubiquitination of glycoproteins, is involved in the endoplasmic reticulum-associated degradation pathway. In SCF ubiquitin ligases, a diverse array of F-box proteins confers substrate speci ...

    The ubiquitin ligase complex SCF(Fbs1), which contributes to the ubiquitination of glycoproteins, is involved in the endoplasmic reticulum-associated degradation pathway. In SCF ubiquitin ligases, a diverse array of F-box proteins confers substrate specificity. Fbs1/Fbx2, a member of the F-box protein family, recognizes high-mannose oligosaccharides. To elucidate the structural basis of SCF(Fbs1) function, we determined the crystal structures of the Skp1-Fbs1 complex and the sugar-binding domain (SBD) of the Fbs1-glycoprotein complex. The mechanistic model indicated by the structures appears to be well conserved among the SCF ubiquitin ligases. The structure of the SBD-glycoprotein complex indicates that the SBD primarily recognizes Man(3)GlcNAc(2), thereby explaining the broad activity of the enzyme against various glycoproteins. Comparison of two crystal structures of the Skp1-Fbs1 complex revealed the relative motion of a linker segment between the F-box and the SBD domains, which might underlie the ability of the complex to recognize different acceptor lysine residues for ubiquitination.


    Organizational Affiliation

    Department of Biotechnology, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
F-box only protein 2 AC297Mus musculusMutation(s): 0 
Gene Names: Fbxo2Fbs1Fbx2
Find proteins for Q80UW2 (Mus musculus)
Explore Q80UW2 
Go to UniProtKB:  Q80UW2
NIH Common Fund Data Resources
IMPC:  MGI:2446216
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
S-phase kinase-associated protein 1A BD166Homo sapiensMutation(s): 0 
Gene Names: SKP1EMC19OCP2SKP1ATCEB1L
Find proteins for P63208 (Homo sapiens)
Explore P63208 
Go to UniProtKB:  P63208
NIH Common Fund Data Resources
PHAROS:  P63208
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.52 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.942α = 90
b = 109.816β = 90
c = 153.04γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance