4Z2Z

New crystal structure of yeast Ddi1 aspartyl protease reveals substrate engagement mode


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural studies of the yeast DNA damage-inducible protein Ddi1 reveal domain architecture of this eukaryotic protein family.

Trempe, J.F.Saskova, K.G.Siva, M.Ratcliffe, C.D.Veverka, V.Hoegl, A.Menade, M.Feng, X.Shenker, S.Svoboda, M.Kozisek, M.Konvalinka, J.Gehring, K.

(2016) Sci Rep 6: 33671-33671

  • DOI: 10.1038/srep33671
  • Primary Citation of Related Structures:  
    2N7E, 5KES, 4Z2Z

  • PubMed Abstract: 
  • The eukaryotic Ddi1 family is defined by a conserved retroviral aspartyl protease-like (RVP) domain found in association with a ubiquitin-like (UBL) domain. Ddi1 from Saccharomyces cerevisiae additionally contains a ubiquitin-associated (UBA) domain. The substrate specificity and role of the protease domain in the biological functions of the Ddi family remain unclear ...

    The eukaryotic Ddi1 family is defined by a conserved retroviral aspartyl protease-like (RVP) domain found in association with a ubiquitin-like (UBL) domain. Ddi1 from Saccharomyces cerevisiae additionally contains a ubiquitin-associated (UBA) domain. The substrate specificity and role of the protease domain in the biological functions of the Ddi family remain unclear. Yeast Ddi1 has been implicated in the regulation of cell cycle progression, DNA-damage repair, and exocytosis. Here, we investigated the multi-domain structure of yeast Ddi1 using X-ray crystallography, nuclear magnetic resonance, and small-angle X-ray scattering. The crystal structure of the RVP domain sheds light on a putative substrate recognition site involving a conserved loop. Isothermal titration calorimetry confirms that both UBL and UBA domains bind ubiquitin, and that Ddi1 binds K48-linked diubiquitin with enhanced affinity. The solution NMR structure of a helical domain that precedes the protease displays tertiary structure similarity to DNA-binding domains from transcription regulators. Our structural studies suggest that the helical domain could serve as a landing platform for substrates in conjunction with attached ubiquitin chains binding to the UBL and UBA domains.


    Organizational Affiliation

    Groupe de Recherche Axé sur la Structure des Protéines, Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA damage-inducible protein 1A, B146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DDI1VSM1YER143W
EC: 3.4.23
UniProt
Find proteins for P40087 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40087 
Go to UniProtKB:  P40087
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.515α = 90
b = 50.051β = 90
c = 131.562γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
PDB_EXTRACTdata extraction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2016-10-12
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence