5IFR

Structure of the stable UBE2D3-UbDha conjugate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

A cascading activity-based probe sequentially targets E1-E2-E3 ubiquitin enzymes.

Mulder, M.P.Witting, K.Berlin, I.Pruneda, J.N.Wu, K.P.Chang, J.G.Merkx, R.Bialas, J.Groettrup, M.Vertegaal, A.C.Schulman, B.A.Komander, D.Neefjes, J.El Oualid, F.Ovaa, H.

(2016) Nat.Chem.Biol. 12: 523-530

  • DOI: 10.1038/nchembio.2084

  • PubMed Abstract: 
  • Post-translational modifications of proteins with ubiquitin (Ub) and ubiquitin-like modifiers (Ubls), orchestrated by a cascade of specialized E1, E2 and E3 enzymes, control a wide range of cellular processes. To monitor catalysis along these complex ...

    Post-translational modifications of proteins with ubiquitin (Ub) and ubiquitin-like modifiers (Ubls), orchestrated by a cascade of specialized E1, E2 and E3 enzymes, control a wide range of cellular processes. To monitor catalysis along these complex reaction pathways, we developed a cascading activity-based probe, UbDha. Similarly to the native Ub, upon ATP-dependent activation by the E1, UbDha can travel downstream to the E2 (and subsequently E3) enzymes through sequential trans-thioesterifications. Unlike the native Ub, at each step along the cascade, UbDha has the option to react irreversibly with active site cysteine residues of target enzymes, thus enabling their detection. We show that our cascading probe 'hops' and 'traps' catalytically active Ub-modifying enzymes (but not their substrates) by a mechanism diversifiable to Ubls. Our founder methodology, amenable to structural studies, proteome-wide profiling and monitoring of enzymatic activity in living cells, presents novel and versatile tools to interrogate Ub and Ubl cascades.


    Organizational Affiliation

    Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany.,Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands.,Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, the Netherlands.,Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Howard Hughes Medical Institute, Memphis, Tennessee, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 D3
A
151Homo sapiensMutation(s): 0 
Gene Names: UBE2D3 (UBC5C, UBCH5C)
EC: 2.3.2.23
Find proteins for P61077 (Homo sapiens)
Go to Gene View: UBE2D3
Go to UniProtKB:  P61077
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
B
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.125α = 90.00
b = 52.271β = 100.78
c = 53.624γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling

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

Revision History 

  • Version 1.0: 2016-05-11
    Type: Initial release
  • Version 1.1: 2016-06-01
    Type: Database references
  • Version 1.2: 2016-06-29
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence
  • Version 1.4: 2019-02-20
    Type: Advisory, Data collection, Derived calculations
  • Version 1.5: 2019-07-10
    Type: Data collection