3DKB

Crystal Structure of A20, 2.5 angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.246 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.210 (DCC) 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular basis for the unique deubiquitinating activity of the NF-kappaB inhibitor A20

Lin, S.-C.Chung, J.Y.Lamothe, B.Rajashankar, K.Lu, M.Lo, Y.-C.Lam, A.Y.Darnay, B.G.Wu, H.

(2008) J Mol Biol 376: 526-540

  • DOI: https://doi.org/10.1016/j.jmb.2007.11.092
  • Primary Citation of Related Structures:  
    3DKB

  • PubMed Abstract: 

    Nuclear factor kappaB (NF-kappaB) activation in tumor necrosis factor, interleukin-1, and Toll-like receptor pathways requires Lys63-linked nondegradative polyubiquitination. A20 is a specific feedback inhibitor of NF-kappaB activation in these pathways that possesses dual ubiquitin-editing functions. While the N-terminal domain of A20 is a deubiquitinating enzyme (DUB) for Lys63-linked polyubiquitinated signaling mediators such as TRAF6 and RIP, its C-terminal domain is a ubiquitin ligase (E3) for Lys48-linked degradative polyubiquitination of the same substrates. To elucidate the molecular basis for the DUB activity of A20, we determined its crystal structure and performed a series of biochemical and cell biological studies. The structure reveals the potential catalytic mechanism of A20, which may be significantly different from papain-like cysteine proteases. Ubiquitin can be docked onto a conserved A20 surface; this interaction exhibits charge complementarity and no steric clash. Surprisingly, A20 does not have specificity for Lys63-linked polyubiquitin chains. Instead, it effectively removes Lys63-linked polyubiquitin chains from TRAF6 without dissembling the chains themselves. Our studies suggest that A20 does not act as a general DUB but has the specificity for particular polyubiquitinated substrates to assure its fidelity in regulating NF-kappaB activation in the tumor necrosis factor, interleukin-1, and Toll-like receptor pathways.


  • Organizational Affiliation

    Department of Biochemistry, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor, alpha-induced protein 3
A, B, C, D, E
A, B, C, D, E, F
390Homo sapiensMutation(s): 0 
Gene Names: TNFAIP3
EC: 3 (PDB Primary Data), 2.3.2 (UniProt), 3.4.19.12 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P21580 (Homo sapiens)
Explore P21580 
Go to UniProtKB:  P21580
PHAROS:  P21580
GTEx:  ENSG00000118503 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21580
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.246 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.210 (DCC) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.636α = 90
b = 123.636β = 90
c = 143.043γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references