6Y5N

RING-DTC domain of Deltex1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into ADP-ribosylation of ubiquitin by Deltex family E3 ubiquitin ligases.

Chatrin, C.Gabrielsen, M.Buetow, L.Nakasone, M.A.Ahmed, S.F.Sumpton, D.Sibbet, G.J.Smith, B.O.Huang, D.T.

(2020) Sci Adv 6

  • DOI: https://doi.org/10.1126/sciadv.abc0418
  • Primary Citation of Related Structures:  
    6Y5N, 6Y5P

  • PubMed Abstract: 

    Cellular cross-talk between ubiquitination and other posttranslational modifications contributes to the regulation of numerous processes. One example is ADP-ribosylation of the carboxyl terminus of ubiquitin by the E3 DTX3L/ADP-ribosyltransferase PARP9 heterodimer, but the mechanism remains elusive. Here, we show that independently of PARP9, the conserved carboxyl-terminal RING and DTC (Deltex carboxyl-terminal) domains of DTX3L and other human Deltex proteins (DTX1 to DTX4) catalyze ADP-ribosylation of ubiquitin's Gly 76 Structural studies reveal a hitherto unknown function of the DTC domain in binding NAD + Deltex RING domain recruits E2 thioesterified with ubiquitin and juxtaposes it with NAD + bound to the DTC domain to facilitate ADP-ribosylation of ubiquitin. This ubiquitin modification prevents its activation but is reversed by the linkage nonspecific deubiquitinases. Our study provides mechanistic insights into ADP-ribosylation of ubiquitin by Deltex E3s and will enable future studies directed at understanding the increasingly complex network of ubiquitin cross-talk.


  • Organizational Affiliation

    Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase DTX1
A, B
235Homo sapiensMutation(s): 0 
Gene Names: DTX1
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q86Y01 (Homo sapiens)
Explore Q86Y01 
Go to UniProtKB:  Q86Y01
PHAROS:  Q86Y01
GTEx:  ENSG00000135144 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86Y01
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.49α = 90
b = 86.55β = 90
c = 129.83γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
autoPROCdata scaling
SHELXCDphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomA23278
European Research Council (ERC)United Kingdom647849

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2020-10-07
    Changes: Structure summary