Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Functional 3D architecture in an intrinsically disordered E3 ligase domain facilitates ubiquitin transfer

Paul Murphy, Yingqi Xu, Sarah L. Rouse, View ORCID ProfileSteve J. Matthews, J Carlos Penedo, View ORCID ProfileRonald T. Hay
doi: https://doi.org/10.1101/831362
Paul Murphy
1Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, DD1 5EH, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yingqi Xu
2Centre for Structural Biology, Department of Life Sciences, Imperial College London SW7 2AZ, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sarah L. Rouse
2Centre for Structural Biology, Department of Life Sciences, Imperial College London SW7 2AZ, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Steve J. Matthews
2Centre for Structural Biology, Department of Life Sciences, Imperial College London SW7 2AZ, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Steve J. Matthews
J Carlos Penedo
3SUPA School of Physics and Astronomy, University of St. Andrews, KY16 9SS, UK
4Biomedical Sciences Research Complex, School of Biology, University of St. Andrews, KY16 9ST, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ronald T. Hay
1Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, DD1 5EH, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Ronald T. Hay
  • For correspondence: r.t.hay@dundee.ac.uk
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Post-translational modification of proteins with ubiquitin represents a widely used mechanism for cellular regulation. Ubiquitin is activated by an E1 enzyme, transferred to an E2 conjugating enzyme and covalently linked to substrates by one of an estimated 600 E3 ligases (1). RING E3 ligases play a pivotal role in selecting substrates and priming the ubiquitin loaded E2 (E2~Ub) for catalysis (2,3). RING E3 RNF4 is a SUMO targeted ubiquitin ligase (4) with important roles in arsenic therapy for cancer (4,5) and in DNA damage responses (6,7). RNF4 has a RING domain and a substrate recognition domain containing multiple SUMO Interaction Motifs (SIMs) embedded in a region thought to be intrinsically disordered (8). While molecular details of SUMO recognition by the SIMs (8–10) and RING engagement of ubiquitin loaded E2 (3,11–15) have been determined, the mechanism by which SUMO substrate is delivered to the RING to facilitate ubiquitin transfer is an important question to be answered. Here, we show that the intrinsically disordered substrate-recognition domain of RNF4 maintains the SIMs in a compact global architecture that facilitates SUMO binding, while a highly-basic region positions substrate for nucleophilic attack on RING-bound ubiquitin loaded E2. Contrary to our expectation that the substrate recognition domain of RNF4 was completely disordered, distance measurements using single molecule Fluorescence Resonance Energy Transfer (smFRET) and NMR paramagnetic relaxation enhancement (PRE) revealed that it adopts a defined conformation primed for SUMO interaction. Mutational and biochemical analysis indicated that electrostatic interactions involving the highly basic region linking the substrate recognition and RING domains juxtaposed those regions and mediated substrate ubiquitination. Our results offer insight into a key step in substrate ubiquitination by a member of the largest ubiquitin ligase subtype and reveal how a defined architecture within a disordered region contributes to E3 ligase function.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted November 05, 2019.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Functional 3D architecture in an intrinsically disordered E3 ligase domain facilitates ubiquitin transfer
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Functional 3D architecture in an intrinsically disordered E3 ligase domain facilitates ubiquitin transfer
Paul Murphy, Yingqi Xu, Sarah L. Rouse, Steve J. Matthews, J Carlos Penedo, Ronald T. Hay
bioRxiv 831362; doi: https://doi.org/10.1101/831362
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Functional 3D architecture in an intrinsically disordered E3 ligase domain facilitates ubiquitin transfer
Paul Murphy, Yingqi Xu, Sarah L. Rouse, Steve J. Matthews, J Carlos Penedo, Ronald T. Hay
bioRxiv 831362; doi: https://doi.org/10.1101/831362

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Biophysics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4112)
  • Biochemistry (8814)
  • Bioengineering (6518)
  • Bioinformatics (23459)
  • Biophysics (11789)
  • Cancer Biology (9206)
  • Cell Biology (13321)
  • Clinical Trials (138)
  • Developmental Biology (7434)
  • Ecology (11409)
  • Epidemiology (2066)
  • Evolutionary Biology (15147)
  • Genetics (10436)
  • Genomics (14042)
  • Immunology (9170)
  • Microbiology (22152)
  • Molecular Biology (8811)
  • Neuroscience (47563)
  • Paleontology (350)
  • Pathology (1428)
  • Pharmacology and Toxicology (2491)
  • Physiology (3730)
  • Plant Biology (8079)
  • Scientific Communication and Education (1437)
  • Synthetic Biology (2220)
  • Systems Biology (6037)
  • Zoology (1253)