PDBsum entry 2rsu

Protein binding

PDB id: 2rsu

Contents

Protein chain

76 a.a.

PDB id:

2rsu

Name:

Protein binding

Title:

Alternative structure of ubiquitin

Structure:

Ubiquitin. Chain: a. Engineered: yes. Mutation: yes

Source:

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

NMR struc:

20 models

Authors:

S.Kitazawa,T.Kameda,M.Yagi-Utsumi,K.Kato,R.Kitahara

Key ref:

S.Kitazawa et al. (2013). Solution structure of the Q41N variant of ubiquitin as a model for the alternatively folded N2 state of ubiquitin. Biochemistry, 52, 1874-1885. PubMed id: 23421577 DOI: 10.1021/bi301420m

Date:

15-Jun-12 Release date: 27-Mar-13

Protein chain

P62987  (RL40_HUMAN) -  Ubiquitin-ribosomal protein eL40 fusion protein from Homo sapiens

Seq: 128 a.a.

Struc: 76 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1021/bi301420m

Biochemistry 52:1874-1885 (2013)

PubMed id: 23421577

Solution structure of the Q41N variant of ubiquitin as a model for the alternatively folded N2 state of ubiquitin.

S.Kitazawa, T.Kameda, M.Yagi-Utsumi, K.Sugase, N.J.Baxter, K.Kato, M.P.Williamson, R.Kitahara.

ABSTRACT

It is becoming increasingly clear that proteins transiently populate high-energy excited states as a necessary requirement for function. Here, we demonstrate that rational mutation based on the characteristics of the structure and dynamics of proteins obtained from pressure experiments is a new strategy for amplifying particular fluctuations in proteins. We have previously shown that ubiquitin populates a high-energy conformer, N2, at high pressures. Here, we show that the Q41N mutation favors N2: high-pressure nuclear magnetic resonance (NMR) shows that N2 is ∼70% populated in Q41N but only ∼20% populated in the wild type at ambient pressure. This allows us to characterize the structure of N2, in which α1-helix, the following loop, β3-strand, and β5-strand change their orientations relative to the remaining regions. Conformational fluctuation on the microsecond time scale, characterized by (15)N spin relaxation NMR analysis, is markedly increased for these regions of the mutant. The N2 conformers produced by high pressure and by the Q41N mutation are quite similar in both structure and dynamics. The conformational change to produce N2 is proposed to be a novel dynamic feature beyond the known recognition dynamics of the protein. Indeed, it is orthogonal to that seen when proteins containing a ubiquitin-interacting motif bind at the hydrophobic patch of ubiquitin but matches changes seen on binding to the E2 conjugating enzyme. More generally, structural and dynamic effects of hydrodynamic pressure are shown to be useful for characterizing functionally important intermediates.