MINDY3: a hub between protein quality control and DNA repair

A team of researchers from the MRC Protein Phosphorylation and Ubiquitylation Unit at the University of Dundee, together with collaborators from the ETH Zürich, the Malopolska Centre of Biotechnology and the University of Veterinary Medicine Vienna, report a new link between protein quality control and DNA damage responses.

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The work centers on MINDY3, a deubiquitinase enzyme, and reveals that it carries a distinctive EF-hand region that acts as a novel ubiquitin-binding domain. This EF-hand contains three binding surfaces that let MINDY3 recognize and cleave long polyubiquitin chains more efficiently, a key step in controlling protein fate inside cells. Crucially, the EF-hand of MINDY3 binds not only to ubiquitin chains but also to the UBL (ubiquitin-like) domains of RAD23A and RAD23B, proteins that help shuttle ubiquitylated cargo to the proteasome for degradation. This discovery links MINDY3 to the RAD23–proteasome axis, guiding MINDY3 to sites where DNA damage has occurred and suggesting a coordinated role in protein quality control during DNA repair processes. Sebastian Glatt, professor of systems genetics at Vetmeduni and group leader at the Małopolska Centre of Biotechnology (MCB) at the Jagiellonian University, sums up: "The key takeaway is that cells have intricate “quality-control” systems to manage damaged proteins and to repair DNA - our work uncovers a new piece of that complex molecular puzzle."

Structure meets cell biology – MINDY3 at the damage site

The research team solved the crystal structure of the MINDY3 EF-hand in complex with the RAD23A UBL domain, revealing the molecular details of this interaction and identifying specific interface residues that are essential for binding. These structural insights explain how MINDY3 recognizes RAD23A (and RAD23B) while remaining distinct from other ubiquitin interactions.

Guided by RAD23: MINDY3 at the site of DNA repair

In cellular experiments, RAD23A/B influence where MINDY3 localizes when DNA damage is present, supporting a model in which MINDY3 can deubiquitylate RAD23-bound substrates at damage sites, potentially shaping the fate of those proteins during repair. The study uses a multi-disciplinary approach—biochemistry, structural biology, and cell biology—to build a comprehensive picture. Techniques include crystallography to map the binding interface, isothermal titration calorimetry (ITC) to measure interactions, pull-downs to confirm partnerships, and live-cell imaging to track MINDY3’s recruitment to DNA lesions. Together, these methods support a model where the MINDY3 EF-hand acts as a dedicated ubiquitin-binding module that recognizes long ubiquitin chains and couples this signaling to DNA repair pathways via RAD23A/B.

The article „The EF-hand domain of MINDY3 is a ubiquitin and RAD23 UBL-binding domain.” by Armstrong LA, McFarland MR, O'Dea R, Krutyholowa R, Gorka M, Carroll T, Glatt S and Kulathu Y. was published in EMBO Reports.

Scientific article

Rückfragenkontakt:
Univ.-Prof. Dr. Sebastian Glatt
Zentrum für Biologische Wissenschaften
Veterinärmedizinische Universität Wien (Vetmeduni)
Sebastian.Glatt@vetmeduni.ac.at

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