5DFL

Crystal structure of Ube2K~Ubiquitin conjugate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The molecular basis of lysine 48 ubiquitin chain synthesis by Ube2K.

Middleton, A.J.Day, C.L.

(2015) Sci Rep 5: 16793-16793

  • DOI: 10.1038/srep16793

  • PubMed Abstract: 
  • The post-translational modification of proteins by ubiquitin is central to the regulation of eukaryotic cells. Substrate-bound ubiquitin chains linked by lysine 11 and 48 target proteins to the proteasome for degradation and determine protein abundan ...

    The post-translational modification of proteins by ubiquitin is central to the regulation of eukaryotic cells. Substrate-bound ubiquitin chains linked by lysine 11 and 48 target proteins to the proteasome for degradation and determine protein abundance in cells, while other ubiquitin chain linkages regulate protein interactions. The specificity of chain-linkage type is usually determined by ubiquitin-conjugating enzymes (E2s). The degradative E2, Ube2K, preferentially catalyses formation of Lys48-linked chains, but like most E2s, the molecular basis for chain formation is not well understood. Here we report the crystal structure of a Ube2K~ubiquitin conjugate and demonstrate that even though it is monomeric, Ube2K can synthesize Lys48-linked ubiquitin chains. Using site-directed mutagenesis and modelling, our studies reveal a molecular understanding of the catalytic complex and identify key features required for synthesis of degradative Lys48-linked chains. The position of the acceptor ubiquitin described here is likely conserved in other E2s that catalyse Lys48-linked ubiquitin chain synthesis.


    Organizational Affiliation

    Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
B
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 K
A
200Homo sapiensMutation(s): 3 
Gene Names: UBE2K (HIP2, LIG)
EC: 2.3.2.23
Find proteins for P61086 (Homo sapiens)
Go to Gene View: UBE2K
Go to UniProtKB:  P61086
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: 2.1 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 146.324α = 90.00
b = 37.557β = 90.43
c = 61.001γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Marsden Fund, Royal Society of New ZealandNew Zealand--

Revision History 

  • Version 1.0: 2015-12-02
    Type: Initial release
  • Version 1.1: 2015-12-09
    Type: Database references