5OXI

C-terminally retracted ubiquitin L67S mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An invisible ubiquitin conformation is required for efficient phosphorylation by PINK1.

Gladkova, C.Schubert, A.F.Wagstaff, J.L.Pruneda, J.N.Freund, S.M.Komander, D.

(2017) EMBO J. 36: 3555-3572

  • DOI: 10.15252/embj.201797876
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Ser/Thr protein kinase PINK1 phosphorylates the well-folded, globular protein ubiquitin (Ub) at a relatively protected site, Ser65. We previously showed that Ser65 phosphorylation results in a conformational change in which Ub adopts a dynamic eq ...

    The Ser/Thr protein kinase PINK1 phosphorylates the well-folded, globular protein ubiquitin (Ub) at a relatively protected site, Ser65. We previously showed that Ser65 phosphorylation results in a conformational change in which Ub adopts a dynamic equilibrium between the known, common Ub conformation and a distinct, second conformation wherein the last β-strand is retracted to extend the Ser65 loop and shorten the C-terminal tail. We show using chemical exchange saturation transfer (CEST) nuclear magnetic resonance experiments that a similar, C-terminally retracted (Ub-CR) conformation also exists at low population in wild-type Ub. Point mutations in the moving β5 and neighbouring β-strands shift the Ub/Ub-CR equilibrium. This enabled functional studies of the two states, and we show that while the Ub-CR conformation is defective for conjugation, it demonstrates improved binding to PINK1 through its extended Ser65 loop, and is a superior PINK1 substrate. Together our data suggest that PINK1 utilises a lowly populated yet more suitable Ub-CR conformation of Ub for efficient phosphorylation. Our findings could be relevant for many kinases that phosphorylate residues in folded protein domains.


    Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Medical Research Council Laboratory of Molecular Biology, Cambridge, UK dk@mrc-lmb.cam.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin L67S mutant
A, B
76Homo sapiensMutation(s): 1 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.193 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 41.055α = 90.00
b = 48.813β = 90.00
c = 74.401γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomU105192732
European Research CouncilUnited Kingdom309756
Lister Institute for Preventive MedicineUnited Kingdom--

Revision History 

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2017-12-27
    Type: Database references