PDBsum entry 3hcs

Signaling protein

PDB id: 3hcs

Contents

Protein chains

157 a.a. *

Metals

_ZN ×10

Waters ×196

* Residue conservation analysis

PDB id:

3hcs

Name:

Signaling protein

Title:

Crystal structure of the n-terminal domain of traf6

Structure:

Tnf receptor-associated factor 6. Chain: a, b. Fragment: ring and zinc fingers 1-3: unp residues 50-211. Synonym: interleukin-1 signal transducer, ring finger protein 85. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: rnf85, traf6. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.20Å R-factor: 0.229 R-free: 0.271

Authors:

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,H.Wu

Key ref:

Q.Yin et al. (2009). E2 interaction and dimerization in the crystal structure of TRAF6. Nat Struct Biol, 16, 658-666. PubMed id: 19465916 DOI: 10.1038/nsmb.1605

Date:

06-May-09 Release date: 26-May-09

Protein chains

Q9Y4K3  (TRAF6_HUMAN) -  TNF receptor-associated factor 6 from Homo sapiens

Seq: 522 a.a.

Struc: 157 a.a.

Enzyme reactions

• Enzyme class: E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.
• 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

DOI no: 10.1038/nsmb.1605

Nat Struct Biol 16:658-666 (2009)

PubMed id: 19465916

E2 interaction and dimerization in the crystal structure of TRAF6.

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, H.Wu.

ABSTRACT

Tumor necrosis factor (TNF) receptor-associated factor (TRAF)-6 mediates Lys63-linked polyubiquitination for NF-kappaB activation via its N-terminal RING and zinc finger domains. Here we report the crystal structures of TRAF6 and its complex with the ubiquitin-conjugating enzyme (E2) Ubc13. The RING and zinc fingers of TRAF6 assume a rigid, elongated structure. Interaction of TRAF6 with Ubc13 involves direct contacts of the RING and the preceding residues, and the first zinc finger has a structural role. Unexpectedly, this region of TRAF6 is dimeric both in the crystal and in solution, different from the trimeric C-terminal TRAF domain. Structure-based mutagenesis reveals that TRAF6 dimerization is crucial for polyubiquitin synthesis and autoubiquitination. Fluorescence resonance energy transfer analysis shows that TRAF6 dimerization induces higher-order oligomerization of full-length TRAF6. The mismatch of dimeric and trimeric symmetry may provide a mode of infinite oligomerization that facilitates ligand-dependent signal transduction of many immune receptors.

Selected figure(s)

Figure 2.
(a) Ribbon diagram of the TRAF6 RZ[1]-Ubc13 complex. The Z[2] and Z[3] domains are modeled based on superposition of the TRAF6 RZ[1]–Ubc13 complex with the TRAF6 RZ[123] structure and are shown in gray. (b) Detailed interaction between TRAF6 and Ubc13. TRAF6 is shown in magenta with the carbon atoms of its side chains in yellow. Ubc13 is shown in orange with the carbon atoms of its side chains in gray. (c) Superimposed gel filtration profiles of Ubc13 mixed with wild-type (WT) or mutant TRAF6 RZ[123] designed to disrupt the interaction. Approximate elution positions of molecular weight standards are shown. (d) Yeast two-hybrid experiments on the interaction between Ubc13 and full-length TRAF2, TRAF3, TRAF5, TRAF6 (positive control) and its RING mutant C70A (negative control). (e) Superimposed gel filtration profiles of Ubc13 mixed with wild-type or mutant TRAF6 RZ[123] with interface residues switched to the corresponding sequences in other TRAFs: I72A (mutation to the corresponding TRAF2 sequence), I72K (TRAF3), I72F (TRAF5), L74H (TRAF3 and TRAF5) and L74R (TRAF2). Approximate elution positions of molecular weight standards are shown. (f) Promotion of polyubiquitin chain synthesis by wild-type and mutant TRAF6 RZ[123] in the presence of the E2 complex Ubc13–Uev1A and E1.

Figure 3.
(a) TRAF6 mutants defective in Ubc13 interaction failed to rescue IL-1–induced TRAF6 autoubiquitination in TRAF6-deficient MEFs. The indicated stable cells lines were treated with IL-1 (1 ng ml^-1) for the indicated times and the clarified lysates were immunoblotted with the indicated antibodies. (b) TRAF6 mutants defective in Ubc13 interaction failed to rescue IL-1–induced IKK activation and I B phosphorylation in Traf6^-/- MEFs. IB, immunoblot; WT, wild type.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2009, 16, 658-666) copyright 2009.

Figures were selected by an automated process.