4ONL

Crystal structure of human Mms2/Ubc13_D81N, R85S, A122V, N123P


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Covalent Inhibition of Ubc13 Affects Ubiquitin Signaling and Reveals Active Site Elements Important for Targeting.

Hodge, C.D.Edwards, R.A.Markin, C.J.McDonald, D.Pulvino, M.Huen, M.S.Zhao, J.Spyracopoulos, L.Hendzel, M.J.Glover, J.N.

(2015) Acs Chem.Biol. 10: 1718-1728

  • DOI: 10.1021/acschembio.5b00222
  • Primary Citation of Related Structures:  4ONM, 4ONN

  • PubMed Abstract: 
  • Ubc13 is an E2 ubiquitin conjugating enzyme that functions in nuclear DNA damage signaling and cytoplasmic NF-κB signaling. Here, we present the structures of complexes of Ubc13 with two inhibitors, NSC697923 and BAY 11-7082, which inhibit DNA damage ...

    Ubc13 is an E2 ubiquitin conjugating enzyme that functions in nuclear DNA damage signaling and cytoplasmic NF-κB signaling. Here, we present the structures of complexes of Ubc13 with two inhibitors, NSC697923 and BAY 11-7082, which inhibit DNA damage and NF-κB signaling in human cells. NSC697923 and BAY 11-7082 both inhibit Ubc13 by covalent adduct formation through a Michael addition at the Ubc13 active site cysteine. The resulting adducts of both compounds exploit a binding groove unique to Ubc13. We developed a Ubc13 mutant which resists NSC697923 inhibition and, using this mutant, we show that the inhibition of cellular DNA damage and NF-κB signaling by NSC697923 is largely due to specific Ubc13 inhibition. We propose that unique structural features near the Ubc13 active site could provide a basis for the rational development and design of specific Ubc13 inhibitors.


    Organizational Affiliation

    †Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 variant 2
A
153Homo sapiensGene Names: UBE2V2 (MMS2, UEV2)
Find proteins for Q15819 (Homo sapiens)
Go to Gene View: UBE2V2
Go to UniProtKB:  Q15819
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 N
B
160Homo sapiensGene Names: UBE2N (BLU)
EC: 2.3.2.23
Find proteins for P61088 (Homo sapiens)
Go to Gene View: UBE2N
Go to UniProtKB:  P61088
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.933α = 90.00
b = 74.942β = 90.00
c = 92.055γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-08-05
    Type: Database references