PDBsum entry 3dkb

Hydrolase

PDB id: 3dkb

Contents

Protein chain

(+ 0 more) 352 a.a. *

* Residue conservation analysis

PDB id:

3dkb

Name:

Hydrolase

Title:

Crystal structure of a20, 2.5 angstrom

Structure:

Tumor necrosis factor, alpha-induced protein 3. Chain: a, b, c, d, e, f. Fragment: unp residues 1-370. Synonym: DNA-binding protein a20, zinc finger protein a20. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: tnfaip3. Expressed in: escherichia coli.

Resolution:

2.50Å R-factor: 0.200 R-free: 0.246

Authors:

S.-C.Lin,J.Y.Chung,Y.-C.Lo,H.Wu

Key ref:

S.C.Lin et al. (2008). Molecular basis for the unique deubiquitinating activity of the NF-kappaB inhibitor A20. J Mol Biol, 376, 526-540. PubMed id: 18164316 DOI: 10.1016/j.jmb.2007.11.092

Date:

24-Jun-08 Release date: 08-Jul-08

Protein chains

P21580  (TNAP3_HUMAN) -  Tumor necrosis factor alpha-induced protein 3 from Homo sapiens

Seq: 790 a.a.

Struc: 352 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.3.2.- - ?????
• Enzyme class 2: E.C.3.4.19.12 - ubiquitinyl hydrolase 1.
• Reaction: Thiol-dependent hydrolysis of ester, thiolester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1016/j.jmb.2007.11.092

J Mol Biol 376:526-540 (2008)

PubMed id: 18164316

Molecular basis for the unique deubiquitinating activity of the NF-kappaB inhibitor A20.

S.C.Lin, J.Y.Chung, B.Lamothe, K.Rajashankar, M.Lu, Y.C.Lo, A.Y.Lam, B.G.Darnay, H.Wu.

ABSTRACT

Nuclear factor kappaB (NF-kappaB) activation in tumor necrosis factor, interleukin-1, and Toll-like receptor pathways requires Lys63-linked nondegradative polyubiquitination. A20 is a specific feedback inhibitor of NF-kappaB activation in these pathways that possesses dual ubiquitin-editing functions. While the N-terminal domain of A20 is a deubiquitinating enzyme (DUB) for Lys63-linked polyubiquitinated signaling mediators such as TRAF6 and RIP, its C-terminal domain is a ubiquitin ligase (E3) for Lys48-linked degradative polyubiquitination of the same substrates. To elucidate the molecular basis for the DUB activity of A20, we determined its crystal structure and performed a series of biochemical and cell biological studies. The structure reveals the potential catalytic mechanism of A20, which may be significantly different from papain-like cysteine proteases. Ubiquitin can be docked onto a conserved A20 surface; this interaction exhibits charge complementarity and no steric clash. Surprisingly, A20 does not have specificity for Lys63-linked polyubiquitin chains. Instead, it effectively removes Lys63-linked polyubiquitin chains from TRAF6 without dissembling the chains themselves. Our studies suggest that A20 does not act as a general DUB but has the specificity for particular polyubiquitinated substrates to assure its fidelity in regulating NF-kappaB activation in the tumor necrosis factor, interleukin-1, and Toll-like receptor pathways.

Selected figure(s)

Figure 4.
Fig. 4. The predicted interaction of A20 with ubiquitin. (a and b) Mapping of conserved residues on the A20 surface. The location of the active site is circled. (c) Ribbon diagram of A20 with modeled ubiquitins. The locations of the ubiquitin based on the HAUSP–ubiquitin and Yuh1–ubiquitin complexes are shown in gray and orange, respectively. The location of the ubiquitin after adjustment to avoid steric clash is shown in yellow. (d) Surface presentation of A20 shown in complex with the modeled ubiquitin in a ribbon diagram. The active site is circled. (e) Electrostatic surface presentation of A20 shown in complex with the modeled ubiquitin in a ribbon diagram. The ubiquitin-binding site is mostly negatively charged. (f and g) The model of the A20–ubiquitin complex shown with A20 in a ribbon diagram and the ubiquitin in an electrostatic surface representation. The positive electrostatic potential of the side of ubiquitin in contact with A20 is shown. (h) The proposed oxyanion hole construction of A20 by the main-chain amides of Cys103, Gly101, and Asp100. The corresponding regions in Yuh1 and HAUSP are superimposed and shown.

Figure 6.
Fig. 6. Structure-based mutational analyses. (a) Cleavage of Lys48-linked polyubiquitin chains by wild-type and mutant A20. (b) Cleavage of Lys48-linked diubiquitin by wild-type and mutant A20. (c) Deubiquitination of Lys63-linked polyubiquitinated GST-TRAF6 by wild-type and mutant A20. The left panel shows the appearance of ubiquitin chains in the supernatant of glutathione beads. The right panel shows the decrease in the polyubiquitination of GST-TRAF6 bound to glutathione beads.

The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2008, 376, 526-540) copyright 2008.

Figures were selected by an automated process.