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 
  • R-Value Observed: 0.173 

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:  
    4ONL, 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 and NF-κB signaling in human cells ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 variant 2A153Homo sapiensMutation(s): 0 
Gene Names: MMS2, UBE2V2, UEV2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15819 (Homo sapiens)
Explore Q15819 
Go to UniProtKB:  Q15819
PHAROS:  Q15819
GTEx:  ENSG00000169139 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15819
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 NB160Homo sapiensMutation(s): 3 
Gene Names: BLU, UBE2N
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P61088 (Homo sapiens)
Explore P61088 
Go to UniProtKB:  P61088
PHAROS:  P61088
GTEx:  ENSG00000177889 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61088
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.933α = 90
b = 74.942β = 90
c = 92.055γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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