6D68

Ube2G1 in complex with ubiquitin variant Ubv.G1.1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Functional Analysis of Ubiquitin-based inhibitors that Target the Backsides of E2 Enzymes.

Garg, P.Ceccarelli, D.F.Keszei, A.F.Kourinov, I.Sicheri, F.Sidhu, S.S.

(2019) J.Mol.Biol. --: --

  • DOI: 10.1016/j.jmb.2019.09.024
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ubiquitin-conjugating E2 enzymes are central to the ubiquitination cascade and have been implicated in cancer and other diseases. Despite strong interest in developing specific E2 inhibitors, the shallow and exposed active site has proven recalcitran ...

    Ubiquitin-conjugating E2 enzymes are central to the ubiquitination cascade and have been implicated in cancer and other diseases. Despite strong interest in developing specific E2 inhibitors, the shallow and exposed active site has proven recalcitrant to targeting with reversible small-molecule inhibitors. Here, we used phage display to generate highly potent and selective ubiquitin variants (UbVs) that target the E2 backside, which is located opposite to the active site. A UbV targeting Ube2D1 did not affect charging but greatly attenuated chain elongation. Likewise, a UbV targeting the E2 variant Ube2V1 did not interfere with the charging of its partner E2 enzyme but inhibited formation of di-ubiquitin. In contrast, a UbV that bound to the backside of Ube2G1 impeded the generation of thioester-linked ubiquitin to the active site cysteine of Ube2G1 by the E1 enzyme. Crystal structures of UbVs in complex with three E2 proteins revealed distinctive molecular interactions in each case, but they also highlighted a common backside pocket that the UbVs utilized for enhanced affinity and specificity. These findings validate the E2 backside as a target for inhibition and provide structural insights to aid inhibitor design and screening efforts.


    Organizational Affiliation

    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada. Electronic address: sicheri@lunenfeld.ca.,Department of Chemistry and Chemical Biology, NE-CAT, Cornell University, Argonne, IL 60439, USA.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada; The Donnelly Centre for Cellular and Biomoleular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada.,Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada; The Donnelly Centre for Cellular and Biomoleular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada. Electronic address: sachdev.sidhu@utoronto.ca.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 G1
A, B
171Homo sapiensMutation(s): 0 
Gene Names: UBE2G1 (UBE2G)
EC: 2.3.2.23
Find proteins for P62253 (Homo sapiens)
Go to Gene View: UBE2G1
Go to UniProtKB:  P62253
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubv.G1.1
C, D
86N/AMutation(s): 10 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A, B
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.213 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 66.537α = 90.00
b = 66.537β = 90.00
c = 225.098γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanadaMOP-136956
Canadian Institutes of Health ResearchCanadaMOP-126129

Revision History 

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2019-11-06
    Type: Data collection, Database references