5F6E

Crystal Structure of human Ubc9 (K48A/K49A/E54A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  
    5F6D, 5F6V, 5F6U, 5F6X, 5F6W, 5F6Y, 5F6E

  • 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. schneeklothjs@mail.nih.gov.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SUMO-conjugating enzyme UBC9A157Homo sapiensMutation(s): 3 
Gene Names: UBE2IUBC9UBCE9
EC: 6.3.2 (PDB Primary Data), 2.3.2 (UniProt)
Find proteins for P63279 (Homo sapiens)
Explore P63279 
Go to UniProtKB:  P63279
NIH Common Fund Data Resources
PHAROS  P63279
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.154 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.873α = 90
b = 35.537β = 112.16
c = 58.151γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-05-04
    Changes: Database references