3O2P

A Dual E3 Mechanism for Rub1 Ligation to Cdc53: Dcn1(P)-Cdc53(WHB)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A dual E3 mechanism for Rub1 ligation to Cdc53.

Scott, D.C.Monda, J.K.Grace, C.R.Duda, D.M.Kriwacki, R.W.Kurz, T.Schulman, B.A.

(2010) Mol Cell 39: 784-796

  • DOI: https://doi.org/10.1016/j.molcel.2010.08.030
  • Primary Citation of Related Structures:  
    3O2P, 3O2U, 3O6B

  • PubMed Abstract: 

    In ubiquitin-like protein (UBL) cascades, a thioester-linked E2∼UBL complex typically interacts with an E3 enzyme for UBL transfer to the target. Here we demonstrate a variant mechanism, whereby the E2 Ubc12 functions with two E3s, Hrt1 and Dcn1, for ligation of the UBL Rub1 to Cdc53's WHB subdomain. Hrt1 functions like a conventional RING E3, with its N terminus recruiting Cdc53 and C-terminal RING activating Ubc12∼Rub1. Dcn1's "potentiating neddylation" domain (Dcn1(P)) acts as an additional E3, reducing nonspecific Hrt1-mediated Ubc12∼Rub1 discharge and directing Ubc12's active site to Cdc53. Crystal structures of Dcn1(P)-Cdc53(WHB) and Ubc12 allow modeling of a catalytic complex, supported by mutational data. We propose that Dcn1's interactions with both Cdc53 and Ubc12 would restrict the otherwise flexible Hrt1 RING-bound Ubc12∼Rub1 to a catalytically competent orientation. Our data reveal mechanisms by which two E3s function synergistically to promote UBL transfer from one E2 to a target.


  • Organizational Affiliation

    Howard Hughes Medical Institute, St Jude Children's Research Hospital, Memphis, TN 38105, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Defective in cullin neddylation protein 1202Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DCN1YLR128WL3111
UniProt
Find proteins for Q12395 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12395 
Go to UniProtKB:  Q12395
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12395
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 53B [auth E]88Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CDC53YDL132WD2190
UniProt
Find proteins for Q12018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12018 
Go to UniProtKB:  Q12018
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12018
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.174 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.157α = 90
b = 57.157β = 90
c = 177.725γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-21
    Changes: Database references
  • Version 1.3: 2018-01-24
    Changes: Structure summary
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description