7BOL

ubiquitin-conjugating enzyme, Ube2D2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

MUL1-RING recruits the substrate, p53-TAD as a complex with UBE2D2-UB conjugate.

Lee, M.S.Lee, S.O.Choi, J.Ryu, M.Lee, M.K.Kim, J.H.Hwang, E.Lee, C.K.Chi, S.W.Ryu, K.S.

(2022) FEBS J 

  • DOI: https://doi.org/10.1111/febs.16360
  • Primary Citation of Related Structures:  
    6M2C, 6M2D, 7BOL

  • PubMed Abstract: 

    The RING domain of MUL1 (RING MUL1 ) alone mediates ubiquitylation of the p53-transactivation domain (TAD p53 ). To elucidate the mechanism underlying the simultaneous recruitment of UBE2D2 and the substrate TAD p53 by RING MUL1 , we determined the complex structure of RING MUL1 :UBE2D2 and studied the interaction between RING MUL1 and TAD p53 in the presence of UBE2D2-UB thioester (UBE2D2~UB) mimetics. The RING MUL1 -binding induced the closed conformation of UBE2D2 S22R/C85S -UB K48R oxyester (UBE2D2 RS -UB R OE ), and strongly accelerated its hydrolysis, which was suppressed by the additional N77A-mutation of UBE2D2. Interestingly, UBE2D2 S22R/N77A/C85S -UB K48R oxyester (UBE2D2 RAS -UB R OE ) already formed a closed conformation in the absence of RING MUL1 . Although TAD p53 exhibited weak binding for RING MUL1 or UBE2D2 alone, its binding affinity was enhanced and even further for RING MUL1 :UBE2D2 and RING MUL1 :UBE2D2 RAS -UB R OE , respectively. The recognition of TAD p53 by RING MUL1 as a complex with UBE2D2~UB is related to the multivalency of the binding events and underlies the ability of RING MUL1 to ubiquitylate the intrinsically disordered protein, TAD p53 .


  • Organizational Affiliation

    Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon, South Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 D2148Homo sapiensMutation(s): 0 
Gene Names: UBE2D2PUBC1UBC4UBC5BUBCH4UBCH5B
EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P62837 (Homo sapiens)
Explore P62837 
Go to UniProtKB:  P62837
PHAROS:  P62837
GTEx:  ENSG00000131508 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62837
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.374α = 90
b = 52.185β = 90
c = 63.27γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2022-04-20
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description