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: 3.10 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 

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
  • Primary Citation of Related Structures:  
    4LCD

  • 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 interactions between the catalytic HECT domain and the E2∼ubiquitin intermediate, which promote formation of a transient, thioester-bonded HECT∼ubiquitin intermediate ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RSP5A, B432Saccharomyces cerevisiae S288CMutation(s): 3 
Gene Names: MDP1NPI1RSP5SYGP-ORF41YER125W
EC: 6.3.2 (PDB Primary Data), 2.3.2.26 (UniProt)
UniProt
Find proteins for P39940 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39940 
Go to UniProtKB:  P39940
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein SNA3C, D24Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: SNA3YJL151CJ0630
UniProt
Find proteins for P14359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14359 
Go to UniProtKB:  P14359
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinE, F83Homo sapiensMutation(s): 1 
Gene Names: UBCUBIQUITIN
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
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: 0.299 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.046α = 90
b = 78.923β = 101.67
c = 96.722γ = 90
Software Package:
Software NamePurpose
ADSCdata 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: 2013-08-14
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Database references