6JX6

Tetrameric form of Smac


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into a HECT-type E3 ligase AREL1 and its ubiquitination activitiesin vitro.

Singh, S.Ng, J.Nayak, D.Sivaraman, J.

(2019) J Biol Chem 294: 19934-19949

  • DOI: 10.1074/jbc.RA119.010327
  • Primary Citation of Related Structures:  
    6JX5, 6JX6

  • PubMed Abstract: 
  • The HECT E3 ligase family comprises three subfamilies: NEDD4 E3 ubiquitin protein ligase (NEDD4), HECT and RLD domain-containing E3 ubiquitin protein ligase (HERC), and "other." Most previous studies have focused on the NEDD4 subfamily. Apoptosis-resista ...

    The HECT E3 ligase family comprises three subfamilies: NEDD4 E3 ubiquitin protein ligase (NEDD4), HECT and RLD domain-containing E3 ubiquitin protein ligase (HERC), and "other." Most previous studies have focused on the NEDD4 subfamily. Apoptosis-resistant E3 ligase 1 (AREL1) belongs to "other" subfamily HECT that inhibits apoptosis by ubiquitinating and degrading proapoptotic proteins. Here, we report the crystal structure of the extended HECT domain of AREL1 (amino acids (aa) 436-823) at 2.4 Å resolution and its ubiquitination of the proapoptotic protein second mitochondria-derived activator of caspase (SMAC). We found that the extended HECT domain adopts an inverted, T-shaped, bilobed conformation and harbors an additional loop (aa 567-573) absent in all other HECT members. We also show that the N-terminal extended region (aa 436-482) preceding the HECT domain is indispensable for its stability and activity and that without this region, the HECT domain becomes inactive. AREL1 ubiquitinated SMAC, primarily on Lys 62 and Lys 191 We solved the crystal structure of the tetrameric form of SMAC to 2.8 Å resolution, revealing the Lys 62 and Lys 191 locations. The AREL1 HECT domain assembled Lys 33 -, Lys 48 -, and Lys 63 -linked polyubiquitin chains. Moreover, E701A substitution in the AREL1 HECT domain substantially increased its autopolyubiquitination and SMAC ubiquitination activity, whereas deletion of the last three amino acids at the C terminus completely abrogated AREL1 autoubiquitination and reduced SMAC ubiquitination. Finally, an AREL1-specific ubiquitin variant inhibited SMAC ubiquitination in vitro Our findings may assist in the development of AREL1 inhibitors that block its anti-apoptotic activity in cancer.


    Organizational Affiliation

    Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, 117543 Singapore dbsjayar@nus.edu.sg.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Diablo homolog, mitochondrial ABCD184Homo sapiensMutation(s): 0 
Gene Names: DIABLOSMAC
Find proteins for Q9NR28 (Homo sapiens)
Explore Q9NR28 
Go to UniProtKB:  Q9NR28
NIH Common Fund Data Resources
PHAROS:  Q9NR28
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.195α = 90
b = 85.403β = 90
c = 114.661γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (Singapore)SingaporeR-154-000-B03-112
Ministry of Education (Singapore)SingaporeR154-000-A72-114

Revision History 

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2020-01-15
    Changes: Database references