2YBF

Complex of Rad18 (Rad6 binding domain) with Rad6b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

E3 Ligase Rad18 Promotes Monoubiquitination Rather Than Ubiquitin Chain Formation by E2 Enzyme Rad6.

Hibbert, R.G.Huang, A.Boelens, R.Sixma, T.K.

(2011) Proc.Natl.Acad.Sci.USA 108: 5590

  • DOI: 10.1073/pnas.1017516108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In ubiquitin conjugation, different combinations of E2 and E3 enzymes catalyse either monoubiquitination or ubiquitin chain formation. The E2/E3 complex Rad6/Rad18 exclusively monoubiquitinates the proliferating cell nuclear antigen (PCNA) to signal ...

    In ubiquitin conjugation, different combinations of E2 and E3 enzymes catalyse either monoubiquitination or ubiquitin chain formation. The E2/E3 complex Rad6/Rad18 exclusively monoubiquitinates the proliferating cell nuclear antigen (PCNA) to signal for "error prone" DNA damage tolerance, whereas a different set of conjugation enzymes is required for ubiquitin chain formation on PCNA. Here we show that human E2 enzyme Rad6b is intrinsically capable of catalyzing ubiquitin chain formation. This activity is prevented during PCNA ubiquitination by the interaction of Rad6 with E3 enzyme Rad18. Using NMR and X-ray crystallography we show that the R6BD of Rad18 inhibits this activity by competing with ubiquitin for a noncovalent "backside" binding site on Rad6. Our findings provide mechanistic insights into how E3 enzymes can regulate the ubiquitin conjugation process.


    Organizational Affiliation

    Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UBIQUITIN-CONJUGATING ENZYME E2 B
A
152Homo sapiensMutation(s): 0 
Gene Names: UBE2B (RAD6B)
EC: 2.3.2.23
Find proteins for P63146 (Homo sapiens)
Go to Gene View: UBE2B
Go to UniProtKB:  P63146
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
E3 UBIQUITIN-PROTEIN LIGASE RAD18
B
27Homo sapiensMutation(s): 0 
Gene Names: RAD18 (RNF73)
EC: 2.3.2.27
Find proteins for Q9NS91 (Homo sapiens)
Go to Gene View: RAD18
Go to UniProtKB:  Q9NS91
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BME
Query on BME

Download SDF File 
Download CCD File 
A
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.199 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 58.210α = 90.00
b = 58.210β = 90.00
c = 167.070γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance