2RSU

Alternative structure of Ubiquitin

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Solution Structure of the Q41N Variant of Ubiquitin as a Model for the Alternatively Folded N2 State of Ubiquitin

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

(2013) Biochemistry 52: 1874-1885

  • DOI: 10.1021/bi301420m

  • PubMed 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 protein ...

    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.

    Organizational Affiliation: 

    College of Pharmaceutical Sciences, Ritsumeikan University , Kusatsu 525-8577, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
A
76Homo sapiensMutation(s): 1 
Gene Names: UBA52 (UBCEP2)
Find proteins for P62987 (Homo sapiens)
Go to Gene View: UBA52
Go to UniProtKB:  P62987
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • Olderado: 2RSU Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-27
    Type: Initial release