4KC9

Structure of HHARI, a RING-IBR-RING ubiquitin ligase: autoinhibition of an Ariadne-family E3 and insights into ligation mechanism


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.274 

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Literature

Structure of HHARI, a RING-IBR-RING Ubiquitin Ligase: Autoinhibition of an Ariadne-Family E3 and Insights into Ligation Mechanism.

Duda, D.M.Olszewski, J.L.Schuermann, J.P.Kurinov, I.Miller, D.J.Nourse, A.Alpi, A.F.Schulman, B.A.

(2013) Structure 21: 1030-1041

  • DOI: 10.1016/j.str.2013.04.019
  • Primary Citation of Related Structures:  
    4KC9, 4KBL

  • PubMed Abstract: 
  • A distinct mechanism for ubiquitin (Ub) ligation has recently been proposed for the RING1-IBR-RING2 (RBR) family of E3s: an N-terminal RING1 domain recruits a thioester-linked intermediate complex between Ub and the E2 UbcH7, and a structurally distinct ...

    A distinct mechanism for ubiquitin (Ub) ligation has recently been proposed for the RING1-IBR-RING2 (RBR) family of E3s: an N-terminal RING1 domain recruits a thioester-linked intermediate complex between Ub and the E2 UbcH7, and a structurally distinct C-terminal RING2 domain displays a catalytic cysteine required for Ub ligation. To obtain insights into RBR E3s, we determined the crystal structure of the human homolog of Ariadne (HHARI), which reveals the individual RING1, IBR, and RING2 domains embedded in superdomains involving sequences specific to the Ariadne RBR subfamily. The central IBR is flanked on one side by RING1, which is exposed and binds UbcH7. On the other side, a C-terminal autoinhibitory "Ariadne domain" masks the RING2 active site. Insights into RBR E3 mechanisms are provided by structure-based mutations that indicate distinct steps of relief from autoinhibition, Ub transfer from E2 to HHARI, and ligation from the HHARI cysteine to a terminal acceptor.


    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase ARIH1 A559Homo sapiensMutation(s): 0 
Gene Names: ARIH1ARIMOP6UBCH7BPHUSSY-27
EC: 6.3.2 (PDB Primary Data), 2.3.2.31 (UniProt)
Find proteins for Q9Y4X5 (Homo sapiens)
Explore Q9Y4X5 
Go to UniProtKB:  Q9Y4X5
NIH Common Fund Data Resources
PHAROS:  Q9Y4X5
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.274 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.126α = 90
b = 96.126β = 90
c = 151.329γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-07-03
    Changes: Database references