HERC2–UBE3A structure uncovers a domain-motif protein network potentially altered in Angelman and related syndromes

UBE3A and HERC2 are two mutually interacting HECT E3 Ubiquitin ligases whose genes are altered in 15q11.2-13.1 Duplication (Dup15q) Syndrome, Angelman Syndrome (AS) and other phenotypically-related mental retardation syndromes. Using quantitative binding assays, X-ray crystallography and sequence conservation analysis, we characterize the core interface of the HERC2-UBE3A complex, involving the RLD2 domain of HERC2 and a “DxDKDxD” sequence from a disordered region of UBE3A. The sequence determinants of the interface are conserved in numerous animals with a central nervous system.

HERC2 also binds similar DxDKDxD motifs within a handful of other proteins relevant to brain development (DOCK10, PCM1, USP35, BAZ2B, ARID4A, ARIP4, RERE and MYT1). We further investigate the interaction of HERC2 with DOCK10, a RAC1- and CDC42-GEF protein that regulates dendritic spine morphogenesis in hippocampal neurons. siRNA-mediated knockdown of HERC2 affects the GEF activity of DOCK10, and mutagenesis of the HERC2-binding motif in DOCK10 disrupts both its GEF activity and its ability to drive dendritic spine formation. In developing brains, an abnormal dosage of either HERC2 or its dominant partner UBE3A may thus alter the proportions of RLD2-mediated complexes, including HERC2-DOCK10, and may thereby perturb dendritic spine morphogenesis and neurodevelopment.

We thank André Mitschler, Arantxa Agote-Arán and Izabela Sumara for insightful scientific discussions and for providing preliminary results. We thank the cell culture platform of the IGBMC for their help in cell culturing. We thank Sandrine Geschier from the IGBMC zebrafish facility.

We thank Pierre Poussin-Courmontagne for the support in protein crystallization and the staff at SOLEIL and SLS for the help and assistance during data collection. We also acknowledge the imaging facility MRI (Montpellier, France), member of the national infrastructure France-BioImaging supported by the French National Research Agency (ANR-10-INBS-04, «Investments for the future»). We are grateful to the Réseaux des Animaleries de Montpellier (RAM-ZEFI) for mouse care and maintenance.

The project was supported by the Ligue contre le cancer (équipe labellisée 2015 to GT), the Agence Nationale de la Recherche (grant ANR-18-CE92-0017, ANR-22-CE44-0018, and ANR-22-CE11-0026 to GT, ANR-19-CE16-0004 to Anne Debant), Dup15q Alliance/Angelman Syndrome Foundation joined Award (2019-2021 to GT). As a member of the IGBMC institute, we benefited from the French Infrastructure for Integrated Structural Biology (FRISBI) ANR-10-INSB-05–01, from Instruct-ERIC, from IdEx Unistra (ANR-10-IDEX-0002), from SFRI-STRAT’US project (ANR 20-SFRI-0012), and from EUR IMCBio (ANR-17-EURE-0023) under the framework of the French Investments for the Future Program as a member of the Interdisciplinary Thematic Institute IMCBio, as part of the ITI 2021–2028 program of the University of Strasbourg, CNRS and Inserm. The Fondation pour la recherche médicale (FRM) supported AD (prix de thèse Pomaret-Delalande sur les maladies rares, 2019-2021) and JWL (SPF202309017619), and Anne Debant (équipe FRM EQU202403018054, 2024-2027).

These authors contributed equally: Auguste Demenge, JiaWen Lim. Equipe Labellisée Ligue 2015, Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France Auguste Demenge, JiaWen Lim, Boglarka Zambo, Gergo Gogl, Alexandra Cousido-Siah, Anna Bonhoure, Camille Kostmann, Judit Osz-Papai, Alberto Podjarny & Gilles Travé Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), University of Montpellier, CNRS, Montpellier, France Arpoudamarie Roc, Christine Fagotto-Kaufmann, Anne Debant & Susanne Schmidt Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France Alastair G. McEwen, Pascal Eberling & Christelle Golzio Facultad Regional Tierra del Fuego, Universidad Tecnologica Nacional, Ushuaia, Tierra del Fuego, Argentina Correspondence to Susanne Schmidt or Gilles Travé.