4LCD

Structure of an Rsp5xUbxSna3 complex: Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3.

Kamadurai, H.B.Qiu, Y.Deng, A.Harrison, J.S.Macdonald, C.Actis, M.Rodrigues, P.Miller, D.J.Souphron, J.Lewis, S.M.Kurinov, I.Fujii, N.Hammel, M.Piper, R.Kuhlman, B.Schulman, B.A.

(2013) Elife 2: e00828-e00828

  • DOI: 10.7554/eLife.00828

  • PubMed Abstract: 
  • Ubiquitination by HECT E3 enzymes regulates myriad processes, including tumor suppression, transcription, protein trafficking, and degradation. HECT E3s use a two-step mechanism to ligate ubiquitin to target proteins. The first step is guided by inte ...

    Ubiquitination by HECT E3 enzymes regulates myriad processes, including tumor suppression, transcription, protein trafficking, and degradation. HECT E3s use a two-step mechanism to ligate ubiquitin to target proteins. The first step is guided by interactions between the catalytic HECT domain and the E2∼ubiquitin intermediate, which promote formation of a transient, thioester-bonded HECT∼ubiquitin intermediate. Here we report that the second step of ligation is mediated by a distinct catalytic architecture established by both the HECT E3 and its covalently linked ubiquitin. The structure of a chemically trapped proxy for an E3∼ubiquitin-substrate intermediate reveals three-way interactions between ubiquitin and the bilobal HECT domain orienting the E3∼ubiquitin thioester bond for ligation, and restricting the location of the substrate-binding domain to prioritize target lysines for ubiquitination. The data allow visualization of an E2-to-E3-to-substrate ubiquitin transfer cascade, and show how HECT-specific ubiquitin interactions driving multiple reactions are repurposed by a major E3 conformational change to promote ligation. DOI:http://dx.doi.org/10.7554/eLife.00828.001.


    Organizational Affiliation

    Department of Structural Biology , St Jude Children's Research Hospital , Memphis , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase RSP5
A, B
432Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 3 
Gene Names: RSP5 (MDP1, NPI1)
EC: 2.3.2.26
Find proteins for P39940 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39940
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein SNA3
C, D
24Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: SNA3
Find proteins for P14359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P14359
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
E, F
83Homo sapiensMutation(s): 1 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.251 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 83.046α = 90.00
b = 78.923β = 101.67
c = 96.722γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
ADSCdata collection
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-14
    Type: Initial release
  • Version 1.1: 2013-08-28
    Type: Database references