Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31261.57 
• Atom Count: 2190 
• Residue Count: 276 
• Unique protein chains: 2

5DFL

Crystal structure of Ube2K~Ubiquitin conjugate

• DOI: 10.2210/pdb5DFL/pdb

• Classification: LIGASE/SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 3 


• Deposited: 2015-08-27 Released: 2015-12-02 
• Deposition Author(s): Middleton, A.J., Day, C.L.
• Funding Organization(s): Marsden Fund, Royal Society of New Zealand 

---

Experimental Data Snapshot

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

Literature

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

Middleton, A.J., Day, C.L.

(2015) Sci Rep 5: 16793-16793

• PubMed: 26592444 
• 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 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
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin	B	76	Homo sapiens	Mutation(s): 0  Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens) Go to Gene View: UBB Go to UniProtKB:  P0CG47

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin-conjugating enzyme E2 K	A	200	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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 = 146.324	α = 90.00
b = 37.557	β = 90.43
c = 61.001	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-08-27 
• Released Date: 2015-12-02 
• Deposition Author(s): Middleton, A.J., Day, C.L.

---

Funding Organization	Location	Grant Number
Marsden Fund, Royal Society of New Zealand	New Zealand	--

Revision History 

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