3O6B

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.258 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Defective in cullin neddylation protein 1 A, C, E, G, I202Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DCN1, YLR128W, L3111
Find proteins for Q12395 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12395 
Go to UniProtKB:  Q12395
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division control protein 53 B, D, F, H, J76Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CDC53, YDL132W, D2190
Find proteins for Q12018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12018 
Go to UniProtKB:  Q12018
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.258 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.914α = 90
b = 123.914β = 90
c = 192.558γ = 120
Software Package:
Software NamePurpose
Necatdata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

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