PDBsum entry 3ns8

Signaling protein

PDB id: 3ns8

Contents

Protein chains

76 a.a.

Ligands

GOL ×2

EPE

Waters ×120

PDB id:

3ns8

Name:

Signaling protein

Title:

Crystal structure of an open conformation of lys48-linked diubiquitin at ph 7.5

Structure:

Ubiquitin. Chain: a, b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: rps27a. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.71Å R-factor: 0.189 R-free: 0.237

Authors:

D.Zhang,N.Laronde-Leblanc,D.Fushman

Key ref:

M.Y.Lai et al. (2012). Structural and biochemical studies of the open state of Lys48-linked diubiquitin. Biochim Biophys Acta, 1823, 2046-2056. PubMed id: 22542781

Date:

01-Jul-10 Release date: 20-Jul-11

Protein chains

P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens

Seq: 685 a.a.

Struc: 76 a.a.

Biochim Biophys Acta 1823:2046-2056 (2012)

PubMed id: 22542781

Structural and biochemical studies of the open state of Lys48-linked diubiquitin.

M.Y.Lai, D.Zhang, N.Laronde-Leblanc, D.Fushman.

ABSTRACT

Ubiquitin (Ub) is a small protein highly conserved among eukaryotes and involved in practically all aspects of eukaryotic cell biology. Polymeric chains assembled from covalently-linked Ub monomers function as molecular signals in the regulation of a host of cellular processes. Our previous studies have shown that the predominant state of Lys48-linked di- and tetra-Ub chains at near-physiological conditions is a closed conformation, in which the Ub-Ub interface is formed by the hydrophobic surface residues of the adjacent Ub units. Because these very residues are involved in (poly)Ub interactions with the majority of Ub-binding proteins, their sequestration at the Ub-Ub interface renders the closed conformation of polyUb binding incompetent. Thus the existence of open conformation(s) and the interdomain motions opening and closing the Ub-Ub interface is critical for the recognition of Lys48-linked polyUb by its receptors. Knowledge of the conformational properties of a polyUb signal is essential for our understanding of its specific recognition by various Ub-receptors. Despite their functional importance, open states of Lys48-linked chains are poorly characterized. Here we report a crystal structure of the open state of Lys48-linked di-Ub. Moreover, using NMR, we examined interactions of the open state of this chain (at pH4.5) with a Lys48-linkage-selective receptor, the UBA2 domain of a shuttle protein hHR23a. Our results show that di-Ub binds UBA2 in the same mode and with comparable affinity as the closed state. Our data suggest a mechanism for polyUb signal recognition, whereby Ub-binding proteins select specific conformations out of the available ensemble of polyUb chain conformations. This article is part of a Special Issue entitled: Ubiquitin Drug Discovery and Diagnostics.