2N7D

Solution structure of the UBL domain of human Ddi2


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 40 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Human DNA-Damage-Inducible 2 Protein Is Structurally and Functionally Distinct from Its Yeast Ortholog.

Siva, M.Svoboda, M.Veverka, V.Trempe, J.F.Hofmann, K.Kozisek, M.Hexnerova, R.Sedlak, F.Belza, J.Brynda, J.Sacha, P.Hubalek, M.Starkova, J.Flaisigova, I.Konvalinka, J.Saskova, K.G.

(2016) Sci Rep 6: 30443-30443

  • DOI: https://doi.org/10.1038/srep30443
  • Primary Citation of Related Structures:  
    2N7D, 5K57

  • PubMed Abstract: 

    Although Ddi1-like proteins are conserved among eukaryotes, their biological functions remain poorly characterized. Yeast Ddi1 has been implicated in cell cycle regulation, DNA-damage response, and exocytosis. By virtue of its ubiquitin-like (UBL) and ubiquitin-associated (UBA) domains, it has been proposed to serve as a proteasomal shuttle factor. All Ddi1-like family members also contain a highly conserved retroviral protease-like (RVP) domain with unknown substrate specificity. While the structure and biological function of yeast Ddi1 have been investigated, no such analysis is available for the human homologs. To address this, we solved the 3D structures of the human Ddi2 UBL and RVP domains and identified a new helical domain that extends on either side of the RVP dimer. While Ddi1-like proteins from all vertebrates lack a UBA domain, we identify a novel ubiquitin-interacting motif (UIM) located at the C-terminus of the protein. The UIM showed a weak yet specific affinity towards ubiquitin, as did the Ddi2 UBL domain. However, the full-length Ddi2 protein is unable to bind to di-ubiquitin chains. While proteomic analysis revealed no activity, implying that the protease requires other factors for activation, our structural characterization of all domains of human Ddi2 sets the stage for further characterization.


  • Organizational Affiliation

    Gilead Sciences and IOCB Research Center, Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein DDI1 homolog 297Homo sapiensMutation(s): 0 
Gene Names: DDI2
EC: 3.4.23
UniProt & NIH Common Fund Data Resources
Find proteins for Q5TDH0 (Homo sapiens)
Explore Q5TDH0 
Go to UniProtKB:  Q5TDH0
PHAROS:  Q5TDH0
GTEx:  ENSG00000197312 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5TDH0
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 40 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-08-03
    Changes: Database references
  • Version 1.2: 2016-08-10
    Changes: Structure summary
  • Version 1.3: 2023-06-14
    Changes: Data collection, Database references, Other
  • Version 1.4: 2024-05-15
    Changes: Data collection, Database references