3DKB

Crystal Structure of A20, 2.5 angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.jmb.2007.11.092

  • 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 pathw ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor, alpha-induced protein 3
A, B, C, D, E, F
390Homo sapiensMutation(s): 0 
Gene Names: TNFAIP3 (OTUD7C)
EC: 2.3.2.-, 3.4.19.12
Find proteins for P21580 (Homo sapiens)
Go to Gene View: TNFAIP3
Go to UniProtKB:  P21580
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.200 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 123.636α = 90.00
b = 123.636β = 90.00
c = 143.043γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
RESOLVEphasing
SCALEPACKdata scaling
SOLVEphasing
ADSCdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description