PDBsum entry 2jy6

Signaling protein

PDB id: 2jy6

Contents

Protein chains

76 a.a. *

52 a.a. *

* Residue conservation analysis

PDB id:

2jy6

Name:

Signaling protein

Title:

Solution structure of the complex of ubiquitin and ubiquilin 1 uba domain

Structure:

Ubiquitin protein. Chain: a. Engineered: yes. Ubiquilin-1. Chain: b. Synonym: protein linking iap with cytoskeleton 1, plic-1, hplic- 1. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ubi1, rpl40a. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Gene: ubqln1, da41, plic1.

NMR struc:

10 models

Authors:

D.Zhang,S.Raasi,D.Fushman

Key ref:

D.Zhang et al. (2008). Affinity makes the difference: nonselective interaction of the UBA domain of Ubiquilin-1 with monomeric ubiquitin and polyubiquitin chains. J Mol Biol, 377, 162-180. PubMed id: 18241885 DOI: 10.1016/j.jmb.2007.12.029

Date:

06-Dec-07 Release date: 18-Mar-08

Protein chain

P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens

Seq: 685 a.a.

Struc: 76 a.a.

Protein chain

Q9UMX0  (UBQL1_HUMAN) -  Ubiquilin-1 from Homo sapiens

Seq: 589 a.a.

Struc: 52 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.?

DOI no: 10.1016/j.jmb.2007.12.029

J Mol Biol 377:162-180 (2008)

PubMed id: 18241885

Affinity makes the difference: nonselective interaction of the UBA domain of Ubiquilin-1 with monomeric ubiquitin and polyubiquitin chains.

D.Zhang, S.Raasi, D.Fushman.

ABSTRACT

Ubiquilin/PLIC proteins belong to the family of UBL-UBA proteins implicated in the regulation of the ubiquitin-dependent proteasomal degradation of cellular proteins. A human presenilin-interacting protein, ubiquilin-1, has been suggested as potential therapeutic target for treating Huntington's disease. Ubiquilin's interactions with mono- and polyubiquitins are mediated by its UBA domain, which is one of the tightest ubiquitin binders among known ubiquitin-binding domains. Here we report the three-dimensional structure of the UBA domain of ubiquilin-1 (UQ1-UBA) free in solution and in complex with ubiquitin. UQ1-UBA forms a compact three-helix bundle structurally similar to other known UBAs, and binds to the hydrophobic patch on ubiquitin with a K(d) of 20 microM. To gain structural insights into UQ1-UBA's interactions with polyubiquitin chains, we have mapped the binding interface between UQ1-UBA and Lys48- and Lys63-linked di-ubiquitins and characterized the strength of UQ1-UBA binding to these chains. Our NMR data show that UQ1-UBA interacts with the individual ubiquitin units in both chains in a mode similar to its interaction with mono-ubiquitin, although with an improved binding affinity for the chains. Our results indicate that, in contrast to UBA2 of hHR23A that has strong binding preference for Lys48-linked chains, UQ1-UBA shows little or no binding selectivity toward a particular chain linkage or between the two ubiquitin moieties in the same chain. The structural data obtained in this study provide insights into the possible structural reasons for the diversity of polyubiquitin chain recognition by UBA domains.

Selected figure(s)

Figure 8.
Fig. 8. Comparison of the structure of (a) UQ1-UBA/monoUb complex derived here with the published structures of monoUb complexes with (b) Dsk2-UBA, (c) Ede1-UBA, and (d) Cue2-CUE1 domains (PDB codes 1WR1, 2G3Q, and 1OTR, respectively). Helices in UBAs are colored green (α1), khaki (α2), and magenta (α3) to guide the eye.

Figure 9.
Fig. 9. Structural models show how UQ1-UBA can bind (a) K63- and (b) K48-linked Ub[2] chains and help rationalize (c and d) the differences in linkage selectivity between UQ1-UBA and hHR23A-UBA2. The structures in (a) and (b) were obtained by superimposition of the UQ1-UBA/Ub complex onto the distal and proximal Ubs of each chain, i.e., assuming that UQ1-UBA interacts with each Ub unit in the same way as with monoUb. The latter is justified by the fact that the CSPs in each Ub in these chains upon UQ1-UBA binding are almost identical with those in monoUb (cf Fig. 2 and Fig. 7). The K63-Ub[2] structure is from Ref. 49, the K48-Ub[2] structure shown in (b) corresponds to a fully open conformation of the chain reported in Refs. [54] and [55]. Comparison of the intermolecular contacts stabilizing the hHR23A-UBA2/K48-Ub[2] complex^30 (c) with those in a hypothetical model of a similar complex for UQ1-UBA (d) shows that the interactions that favor the formation of a 1:1 complex in the former are missing in the latter. The structure model in (d) was obtained by replacing the distal Ub/UBA2 pair in (c) with the Ub/UQ1-UBA structure determined in this study (Fig. 8a); this replacement is justified by the fact that the CSPs observed both in the distal Ub and in the UQ1-UBA are essentially the same as in the monoUb/UQ1-UBA complex. In both structures (c and d), the “canonical” Ub-binding side (loop 1 and helix α3) of the corresponding UBA domain is in contact with the hydrophobic patch on the distal Ub, and only the side chains of residues forming contacts between the UBA and the proximal Ub or the Ub–Ub linker are shown in ball-and-stick representation, colored green (UBA) and cyan (Ub). In all these Ub[2] structures (grey) the distal Ub is on the left, the proximal Ub is on the right. The location of G76 (distal Ub) and the side chain (shown as red stick) of K48 or K63 (proximal Ub) that form the isopeptide bond linking the two Ubs in Ub[2] is indicated. The UBAs bound to the distal and proximal Ubs are colored green and blue, respectively.

The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2008, 377, 162-180) copyright 2008.

Figures were selected by an automated process.