5K9P

Ser20 phosphorylated ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Synthesis of Isomeric Phosphoubiquitin Chains Reveals that Phosphorylation Controls Deubiquitinase Activity and Specificity.

Huguenin-Dezot, N.De Cesare, V.Peltier, J.Knebel, A.Kristaryianto, Y.A.Rogerson, D.T.Kulathu, Y.Trost, M.Chin, J.W.

(2016) Cell Rep 16: 1180-1193

  • DOI: 10.1016/j.celrep.2016.06.064

  • PubMed Abstract: 
  • Ubiquitin is post-translationally modified by phosphorylation at several sites, but the consequences of these modifications are largely unknown. Here, we synthesize multi-milligram quantities of ubiquitin phosphorylated at serine 20, serine 57, and s ...

    Ubiquitin is post-translationally modified by phosphorylation at several sites, but the consequences of these modifications are largely unknown. Here, we synthesize multi-milligram quantities of ubiquitin phosphorylated at serine 20, serine 57, and serine 65 via genetic code expansion. We use these phosphoubiquitins for the enzymatic assembly of 20 isomeric phosphoubiquitin dimers, with different sites of isopeptide linkage and/or phosphorylation. We discover that phosphorylation of serine 20 on ubiquitin converts UBE3C from a dual-specificity E3 ligase into a ligase that primarily synthesizes K48 chains. We profile the activity of 31 deubiquitinases on the isomeric phosphoubiquitin dimers in 837 reactions, and we discover that phosphorylation at distinct sites in ubiquitin can activate or repress cleavage of a particular linkage by deubiquitinases and that phosphorylation at a single site in ubiquitin can control the specificity of deubiquitinases for distinct ubiquitin linkages.


    Organizational Affiliation

    Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, DD1 5EH Dundee, UK.,Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, CB2 OQH Cambridge, UK.,Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, DD1 5EH Dundee, UK. Electronic address: m.trost@dundee.ac.uk.,Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, CB2 OQH Cambridge, UK. Electronic address: chin@mrc-lmb.cam.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
A
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.190 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 49.520α = 90.00
b = 49.520β = 90.00
c = 53.642γ = 120.00
Software Package:
Software NamePurpose
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 KingdomU105181009
Medical Research Council (United Kingdom)United KingdomUPA0241008

Revision History 

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-07-27
    Type: Database references
  • Version 1.2: 2016-08-03
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence