6NJG

Ubiquitin Variant in Complex with Ubiquitin Interacting Motif


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Dimerization of a ubiquitin variant leads to high affinity interactions with a ubiquitin interacting motif.

Manczyk, N.Veggiani, G.Gish, G.D.Yates, B.P.Ernst, A.Sidhu, S.S.Sicheri, F.

(2019) Protein Sci. 28: 848-856

  • DOI: 10.1002/pro.3593

  • PubMed Abstract: 
  • We previously described structural and functional characterization of the first ubiquitin variant (UbV), UbV.v27.1, engineered by phage display to bind with high affinity to a specific ubiquitin interacting motif (UIM). We identified two substitution ...

    We previously described structural and functional characterization of the first ubiquitin variant (UbV), UbV.v27.1, engineered by phage display to bind with high affinity to a specific ubiquitin interacting motif (UIM). We identified two substitutions relative to ubiquitin (Gly10Val/His68Tyr) that were critical for enhancing binding affinity but could only rationalize the mechanism of action of the Tyr68 substitution. Here, we extend our characterization and uncover the mechanism by which the Val10 substitution enhances binding affinity. We show that Val10 in UbV.v27.1 drives UbV dimerization through an intermolecular β-strand exchange. Dimerization serves to increase the contact surface between the UIM and UbV and also affords direct contacts between two UIMs through an overall 2:2 binding stoichiometry. Our identification of the role of Val10 in UbV dimerization suggests a general means for the development of dimeric UbVs with improved affinity and specificity relative to their monomeric UbV counterparts. Statement: Previously, we used phage display to engineer a UbV that bound tightly and specifically to a UIM. Here, we discovered that tight binding is partly due to the dimerization of the UbV, which increases the contact surface between the UbV and UIM. We show that UbV dimerization is dependent on the Gly10Val substitution, and posit that dimerization may provide a general means for engineering UbVs with improved binding properties.


    Organizational Affiliation

    Institute of Biochemistry II, Goethe University, Frankfurt am Main 60590, Germany.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, M5S 3E1 Toronto, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vacuolar protein sorting-associated protein 27
B
24Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VPS27 (DID7, GRD11, SSV17, VPL23, VPT27)
Find proteins for P40343 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40343
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
C
89N/AMutation(s): 18 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.206 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 44.613α = 90.00
b = 44.613β = 90.00
c = 104.343γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHENIXrefinement
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-01-03 
  • Released Date: 2019-03-06 
  • Deposition Author(s): Manczyk, N., Sicheri, F.
  • This entry supersedes: 5UCL

Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanadaFDN-143277

Revision History 

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2019-04-24
    Type: Data collection, Database references