7E62

Mouse TAB2 NZF in complex with Lys6-linked diubiquitin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural basis for specific recognition of K6-linked polyubiquitin chains by the TAB2 NZF domain.

Li, Y., Okatsu, K., Fukai, S., Sato, Y.

(2021) Biophys J 120: 3355-3362

  • DOI: 10.1016/j.bpj.2021.06.037
  • Primary Citation of Related Structures:  
    7E62

  • PubMed Abstract: 

    • TAK1-binding protein 2 (TAB2) has generally been considered to bind specifically to K63-linked polyubiquitin chains via its C-terminal Npl4 zinc-finger (NZF) domain. However, a recent study showed that the NZF domain of TAB2 (TAB2-NZF) could also interact with K6-linked polyubiquitin chains ...

    TAK1-binding protein 2 (TAB2) has generally been considered to bind specifically to K63-linked polyubiquitin chains via its C-terminal Npl4 zinc-finger (NZF) domain. However, a recent study showed that the NZF domain of TAB2 (TAB2-NZF) could also interact with K6-linked polyubiquitin chains. Here, we report the crystal structure of TAB2-NZF in complex with K6-linked diubiquitin (K6-Ub 2 ) at 1.99-Å resolution. TAB2-NZF simultaneously interacts with the distal and proximal ubiquitin moieties of K6-Ub 2 . By comparing the structures of TAB2-NZF in complex with K6-Ub 2 and with K63-linked diubiquitin (K63-Ub 2 ), we reveal that the binding mechanism of TAB2-NZF with K6-Ub 2 is similar to that with K63-Ub 2 , except for the flexible C-terminal region of the distal ubiquitin. Therefore, we conclude that the C-terminal flexibility of the distal ubiquitin contributes to the dual specificity of TAB2-NZF toward K6- and K63-linked ubiquitin chains. This study provides important insights into the functions of K6-linked ubiquitin chains, which are currently unclear.

    Organizational Affiliation: 

    Center for Research on Green Sustainable Chemistry, Tottori, Japan; Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan. Electronic address: yusato@tottori-u.ac.jp.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ubiquitinA,
D [auth H]		76Mus musculusMutation(s): 1 
Gene Names: Rps27a, Uba80, Ubcep1
UniProt
Find proteins for P62983 (Mus musculus)
Explore P62983 
Go to UniProtKB:  P62983
Entity Groups  
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UniProt GroupP62983
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinB,
E [auth I]		77Mus musculusMutation(s): 1 
Gene Names: Rps27a, Uba80, Ubcep1
UniProt
Find proteins for P62983 (Mus musculus)
Explore P62983 
Go to UniProtKB:  P62983
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UniProt GroupP62983
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
TGF-beta-activated kinase 1 and MAP3K7-binding protein 2C,
F [auth J]		55Mus musculusMutation(s): 0 
Gene Names: Tab2, Kiaa0733, Map3k7ip2
UniProt
Find proteins for Q99K90 (Mus musculus)
Explore Q99K90 
Go to UniProtKB:  Q99K90
Entity Groups  
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UniProt GroupQ99K90
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE
Download Ideal Coordinates CCD File 
G [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
H [auth C],
I [auth J]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.694α = 90
b = 76.17β = 90
c = 114.813γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan18H05501

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-18
    Type: Initial release
  • Version 1.1: 2021-11-10
    Changes: Database references