PDBsum entry 2jmd

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protein metals links
Ligase PDB id
Jmol PyMol
Protein chain
63 a.a. *
_ZN ×2
* Residue conservation analysis
PDB id:
Name: Ligase
Title: Solution structure of the ring domain of human traf6
Structure: Tnf receptor-associated factor 6. Chain: a. Fragment: ring-type domain, residues 66-124. Synonym: interleukin 1 signal transducer, ring finger protein 85, htraf6. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: traf6, rnf85. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 50 models
Authors: P.Mercier,M.J.Lewis,D.D.Hau,L.F.Saltibus,W.Xiao, L.Spyracopoulos
Key ref:
P.Mercier et al. (2007). Structure, interactions, and dynamics of the RING domain from human TRAF6. Protein Sci, 16, 602-614. PubMed id: 17327397 DOI: 10.1110/ps.062358007
02-Nov-06     Release date:   10-Apr-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9Y4K3  (TRAF6_HUMAN) -  TNF receptor-associated factor 6
522 a.a.
63 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - RING-type E3 ubiquitin transferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N6- ubiquitinyl-[acceptor protein]-L-lysine
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     immune response   3 terms 
  Biochemical function     ubiquitin-protein ligase activity     2 terms  


DOI no: 10.1110/ps.062358007 Protein Sci 16:602-614 (2007)
PubMed id: 17327397  
Structure, interactions, and dynamics of the RING domain from human TRAF6.
P.Mercier, M.J.Lewis, D.D.Hau, L.F.Saltibus, W.Xiao, L.Spyracopoulos.
A key step in the signaling cascade responsible for activation of the transcription factor NF-kappaB involves Lys63-linked polyubiquitination of TRAF6. Covalent attachment of ubiquitin (Ub) to TRAF6, and subsequent poly(Ub) chain synthesis, is catalyzed by the hUev1a-hUbc13 heterodimer. hUbc13 is a catalytically competent E2 enzyme, and hUev1a is an E2-like protein that binds substrate Ub. The hUev1a-hUbc13 heterodimer is targeted to TRAF6 through interactions between hUbc13 and the N-terminal RING domain from TRAF6. Nuclear magnetic resonance (NMR) spectroscopy was used to determine the solution state structure of the RING domain from human TRAF6, and the interaction between hUbc13 and TRAF6 was characterized using NMR chemical shift mapping. The main-chain dynamics of the RING domain from TRAF6 were studied using (15)N NMR relaxation. Analysis of the main-chain dynamics data indicates that residues within the alpha-helix and beta-sheet of the RING domain are as rigid as regions of canonical secondary structure in larger proteins, consistent with the biological role of RING-domain E3 proteins, which requires that the E3 contain a recognition site for recruitment of E2 ubiquitin conjugation enzymes.
  Selected figure(s)  
Figure 1.
Figure 1. Superposition of the ensemble of 50 NMR structures for
Figure 5.
Figure 5. Main-chain amide relaxation data for TRAF6-RD. (A) (d) 15 N R1 and (s) R2and (B) { 1 H}- 15 N NOE. Elements of secondary
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2007, 16, 602-614) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19465916 Q.Yin, S.C.Lin, B.Lamothe, M.Lu, Y.C.Lo, G.Hura, L.Zheng, R.L.Rich, A.D.Campos, D.G.Myszka, M.J.Lenardo, B.G.Darnay, and H.Wu (2009).
E2 interaction and dimerization in the crystal structure of TRAF6.
  Nat Struct Mol Biol, 16, 658-666.
PDB codes: 3hcs 3hct 3hcu
18617513 B.Lamothe, A.D.Campos, W.K.Webster, A.Gopinathan, L.Hur, and B.G.Darnay (2008).
The RING domain and first zinc finger of TRAF6 coordinate signaling by interleukin-1, lipopolysaccharide, and RANKL.
  J Biol Chem, 283, 24871-24880.  
18817453 C.J.Park, Y.Peng, X.Chen, C.Dardick, D.Ruan, R.Bart, P.E.Canlas, and P.C.Ronald (2008).
Rice XB15, a protein phosphatase 2C, negatively regulates cell death and XA21-mediated innate immunity.
  PLoS Biol, 6, e231.  
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 codes are shown on the right.