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PDBsum entry 3a9k
Go to PDB code: 
protein metals Protein-protein interface(s) links
Signaling protein/metal binding protein PDB id
3a9k

 

 

 

 

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Contents
Protein chains
76 a.a. *
77 a.a. *
29 a.a. *
Metals
_ZN
Waters ×144
* Residue conservation analysis
PDB id:
3a9k
Name: Signaling protein/metal binding protein
Title: Crystal structure of the mouse tab3-nzf in complex with lys63-linked di-ubiquitin
Structure: Ubiquitin. Chain: a. Engineered: yes. Mutation: yes. Ubiquitin. Chain: b. Engineered: yes. Mutation: yes. Mitogen-activated protein kinase kinase kinase 7-
Source: Mus musculus. Mouse. Organism_taxid: 10090. Gene: ubiquitin. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: tab3 (amino acids 688 - 716).
Resolution:
1.40Å     R-factor:   0.189     R-free:   0.218
Authors: Y.Sato,A.Yoshikawa,M.Yamashita,A.Yamagata,S.Fukai
Key ref: Y.Sato et al. (2009). Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by NZF domains of TAB2 and TAB3. Embo J, 28, 3903-3909. PubMed id: 19927120
Date:
29-Oct-09     Release date:   08-Dec-09    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0CG50  (UBC_MOUSE) -  Polyubiquitin-C from Mus musculus
Seq:
Struc: 		 
Seq:
Struc: 		734 a.a.
76 a.a.*
Protein chain
Pfam   ArchSchema ?
P0CG50  (UBC_MOUSE) -  Polyubiquitin-C from Mus musculus
Seq:
Struc: 		 
Seq:
Struc: 		734 a.a.
77 a.a.*
Protein chain
Pfam   ArchSchema ?
Q571K4  (TAB3_MOUSE) -  TGF-beta-activated kinase 1 and MAP3K7-binding protein 3 from Mus musculus
Seq:
Struc: 		 
Seq:
Struc: 		716 a.a.
29 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 

 
Embo J 28:3903-3909 (2009)
PubMed id: 19927120  
 
 
Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by NZF domains of TAB2 and TAB3.
Y.Sato, A.Yoshikawa, M.Yamashita, A.Yamagata, S.Fukai.
 
  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 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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22157957 J.D.Licchesi, J.Mieszczanek, T.E.Mevissen, T.J.Rutherford, M.Akutsu, S.Virdee, F.El Oualid, J.W.Chin, H.Ovaa, M.Bienz, and D.Komander (2012).
An ankyrin-repeat ubiquitin-binding domain determines TRABID's specificity for atypical ubiquitin chains.
  Nat Struct Mol Biol, 19, 62-71.
PDB code: 3zrh
22158122 L.Zhang, X.Ding, J.Cui, H.Xu, J.Chen, Y.N.Gong, L.Hu, Y.Zhou, J.Ge, Q.Lu, L.Liu, S.Chen, and F.Shao (2012).
Cysteine methylation disrupts ubiquitin-chain sensing in NF-κB activation.
  Nature, 481, 204-208.  
22820888 Y.Kulathu, and D.Komander (2012).
Atypical ubiquitylation - the unexplored world of polyubiquitin beyond Lys48 and Lys63 linkages.
  Nat Rev Mol Cell Biol, 13, 508-523.  
21540891 C.Behrends, and J.W.Harper (2011).
Constructing and decoding unconventional ubiquitin chains.
  Nat Struct Mol Biol, 18, 520-528.  
21268159 F.Arnesano, B.D.Belviso, R.Caliandro, G.Falini, S.Fermani, G.Natile, and D.Siliqi (2011).
Crystallographic analysis of metal-ion binding to human ubiquitin.
  Chemistry, 17, 1569-1578.
PDB codes: 3n30 3n32
21332354 J.H.Hurley, and H.Stenmark (2011).
Molecular mechanisms of ubiquitin-dependent membrane traffic.
  Annu Rev Biophys, 40, 119-142.  
20345847 A.S.Shifera (2010).
The zinc finger domain of IKKγ (NEMO) protein in health and disease.
  J Cell Mol Med, 14, 2404-2414.  
21111228 F.Ikeda, N.Crosetto, and I.Dikic (2010).
What determines the specificity and outcomes of ubiquitin signaling?
  Cell, 143, 677-681.  
  20357899 H.Wu, Y.C.Lo, and S.C.Lin (2010).
Recent advances in polyubiquitin chain recognition.
  F1000 Biol Reports, 2, 1-5.  
21095585 I.Bosanac, I.E.Wertz, B.Pan, C.Yu, S.Kusam, C.Lam, L.Phu, Q.Phung, B.Maurer, D.Arnott, D.S.Kirkpatrick, V.M.Dixit, and S.G.Hymowitz (2010).
Ubiquitin binding to A20 ZnF4 is required for modulation of NF-κB signaling.
  Mol Cell, 40, 548-557.
PDB codes: 3oj3 3oj4
20541996 J.M.Winget, and T.Mayor (2010).
The diversity of ubiquitin recognition: hot spots and varied specificity.
  Mol Cell, 38, 627-635.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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