3A9J

Crystal structure of the mouse TAB2-NZF in complex with Lys63-linked di-ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by NZF domains of TAB2 and TAB3

Sato, Y.Yoshikawa, A.Yamashita, M.Yamagata, A.Fukai, S.

(2009) EMBO J 28: 3903-3909

  • DOI: 10.1038/emboj.2009.345
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • TAB2 and TAB3 activate the Jun N-terminal kinase and nuclear factor-kappaB pathways through the specific recognition of Lys 63-linked polyubiquitin chains by its Npl4 zinc-finger (NZF) domain. Here we report crystal structures of the TAB2 and TAB3 NZ ...

    TAB2 and TAB3 activate the Jun N-terminal kinase and nuclear factor-kappaB pathways through the specific recognition of Lys 63-linked polyubiquitin chains by its Npl4 zinc-finger (NZF) domain. Here we report crystal structures of the TAB2 and TAB3 NZF domains in complex with Lys 63-linked diubiquitin at 1.18 and 1.40 A resolutions, respectively. Both NZF domains bind to the distal ubiquitin through a conserved Thr-Phe dipeptide that has been shown to be important for the interaction of the NZF domain of Npl4 with monoubiquitin. In contrast, a surface specific to TAB2 and TAB3 binds the proximal ubiquitin. Both the distal and proximal binding sites of the TAB2 and TAB3 NZF domains recognize the Ile 44-centred hydrophobic patch on ubiquitin but do not interact with the Lys 63-linked isopeptide bond. Mutagenesis experiments show that both binding sites are required to enable binding of Lys 63-linked diubiquitin. We therefore propose a mechanism for the recognition of Lys 63-linked polyubiquitin chains by TAB2 and TAB3 NZF domains in which diubiquitin units are specifically recognized by a single NZF domain.


    Organizational Affiliation

    Structural Biology Laboratory, Life Science Division, Synchrotron Radiation Research Organization, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
A
76Mus musculusMutation(s): 1 
Gene Names: UbiquitinUbc
Find proteins for P0CG50 (Mus musculus)
Go to UniProtKB:  P0CG50
NIH Common Fund Data Resources
IMPC  MGI:98889

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
B
77Mus musculusMutation(s): 1 
Gene Names: UbiquitinUbc
Find proteins for P0CG50 (Mus musculus)
Go to UniProtKB:  P0CG50
NIH Common Fund Data Resources
IMPC  MGI:98889

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase kinase kinase 7-interacting protein 2
C
34Mus musculusMutation(s): 0 
Gene Names: TAB2 (AMINO ACIDS 665 - 693)Tab2Kiaa0733Map3k7ip2
Find proteins for Q99K90 (Mus musculus)
Go to UniProtKB:  Q99K90
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.085α = 90
b = 71.478β = 90
c = 72.029γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SHARPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance