4I6L

Crystal structure of OTUB1 in complex with ubiquitin variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.488 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A strategy for modulation of enzymes in the ubiquitin system.

Ernst, A.Avvakumov, G.Tong, J.Fan, Y.Zhao, Y.Alberts, P.Persaud, A.Walker, J.R.Neculai, A.M.Neculai, D.Vorobyov, A.Garg, P.Beatty, L.Chan, P.K.Juang, Y.C.Landry, M.C.Yeh, C.Zeqiraj, E.Karamboulas, K.Allali-Hassani, A.Vedadi, M.Tyers, M.Moffat, J.Sicheri, F.Pelletier, L.Durocher, D.Raught, B.Rotin, D.Yang, J.Moran, M.F.Dhe-Paganon, S.Sidhu, S.S.

(2013) Science 339: 590-595

  • DOI: 10.1126/science.1230161
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The ubiquitin system regulates virtually all aspects of cellular function. We report a method to target the myriad enzymes that govern ubiquitination of protein substrates. We used massively diverse combinatorial libraries of ubiquitin variants to de ...

    The ubiquitin system regulates virtually all aspects of cellular function. We report a method to target the myriad enzymes that govern ubiquitination of protein substrates. We used massively diverse combinatorial libraries of ubiquitin variants to develop inhibitors of four deubiquitinases (DUBs) and analyzed the DUB-inhibitor complexes with crystallography. We extended the selection strategy to the ubiquitin conjugating (E2) and ubiquitin ligase (E3) enzymes and found that ubiquitin variants can also enhance enzyme activity. Last, we showed that ubiquitin variants can bind selectively to ubiquitin-binding domains. Ubiquitin variants exhibit selective function in cells and thus enable orthogonal modulation of specific enzymatic steps in the ubiquitin system.


    Organizational Affiliation

    Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin thioesterase OTUB1
A
229Homo sapiensMutation(s): 1 
Gene Names: OTUB1 (OTB1, OTU1)
EC: 3.4.19.12
Find proteins for Q96FW1 (Homo sapiens)
Go to Gene View: OTUB1
Go to UniProtKB:  Q96FW1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
B
76Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.488 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.220 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 92.444α = 90.00
b = 109.069β = 90.00
c = 73.238γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-02-06
    Type: Database references
  • Version 1.2: 2013-02-20
    Type: Database references