Mind the metal: a fragment library-derived zinc impurity binds the E2 ubiquitin-conjugating enzyme Ube2T and induces structural rearrangements

DOI: 10.1021/acs.jmedchem.7b01071

Authors: Francesca E. Morreale (University of Dundee) , Andrea Testa (University of Dundee) , Viduth K. Chaugule (University of Dundee) , Alessio Bortoluzzi (University of Dundee) , Alessio Ciulli (University of Dundee) , Helen Walden (University of Dundee)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Journal Of Medicinal Chemistry

State: Published (Approved)
Published: September 2017
Diamond Proposal Number(s): 10071

Abstract: Efforts to develop inhibitors, activators and effectors of biological reactions using small molecule libraries are often hampered by interference compounds, artifacts and false positives that permeate the pool of initial hits. Here we report the discovery of a promising initial hit compound targeting the Fanconi anemia ubiquitin-conjugating enzyme Ube2T and describe its biophysical and biochemical characterization. Analysis of the co-crystal structure led to the identification of a contaminating zinc ion as solely responsible for the observed effects. Zinc binding to the active site cysteine induces a domain swap in Ube2T that leads to cyclic trimerization organized in an open ended linear assembly. Our study serves as a cautionary tale for screening small molecule libraries and provides insights into the structural plasticity of ubiquitin-conjugating enzymes.

Journal Keywords: Ubiquitin-conjugating enzymes; domain swap; false positives; metal-induced oligomerization; ubiquitination; X-ray crystallography

Subject Areas: Chemistry, Biology and Bio-materials


Instruments: I04-1-Macromolecular Crystallography (fixed wavelength)