5F6D

Crystal structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.553 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Insights Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9.

Hewitt, W.M.Lountos, G.T.Zlotkowski, K.Dahlhauser, S.D.Saunders, L.B.Needle, D.Tropea, J.E.Zhan, C.Wei, G.Ma, B.Nussinov, R.Waugh, D.S.Schneekloth, J.S.

(2016) Angew.Chem.Int.Ed.Engl. 55: 5703-5707

  • DOI: 10.1002/anie.201511351
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Conjugation of the small ubiquitin-like modifier (SUMO) to protein substrates is an important disease-associated posttranslational modification, although few inhibitors of this process are known. Herein, we report the discovery of an allosteric small ...

    Conjugation of the small ubiquitin-like modifier (SUMO) to protein substrates is an important disease-associated posttranslational modification, although few inhibitors of this process are known. Herein, we report the discovery of an allosteric small-molecule binding site on Ubc9, the sole SUMO E2 enzyme. An X-ray crystallographic screen was used to identify two distinct small-molecule fragments that bind to Ubc9 at a site distal to its catalytic cysteine. These fragments and related compounds inhibit SUMO conjugation in biochemical assays with potencies of 1.9-5.8 mm. Mechanistic and biophysical analyses, coupled with molecular dynamics simulations, point toward ligand-induced rigidification of Ubc9 as a mechanism of inhibition.


    Organizational Affiliation

    Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SUMO-conjugating enzyme UBC9
A
157Homo sapiensMutation(s): 3 
Gene Names: UBE2I (UBC9, UBCE9)
EC: 2.3.2.-
Find proteins for P63279 (Homo sapiens)
Go to Gene View: UBE2I
Go to UniProtKB:  P63279
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5VJ
Query on 5VJ

Download SDF File 
Download CCD File 
A
6~{H}-benzo[c][1,2]benzothiazine 5,5-dioxide
C12 H9 N O2 S
HXNJMXAYTVQMJT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.553 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.734α = 90.00
b = 35.452β = 111.63
c = 57.979γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
PHENIXrefinement
HKL-3000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-05-04
    Type: Database references
  • Version 1.2: 2017-03-15
    Type: Structure summary