Post-translational Modification that Shines in the Age of Viruses: ISGylation from a Structural Perspective

Post-translational modifications (PTMs) orchestrate the dynamic functional landscape of proteins, governing cellular immunity, signaling, and stress responses. Among these modifications, ISGylation, a ubiquitin-like conjugation process driven by interferon signaling, has emerged as a pivotal regulator of antiviral defense. ISG15 (Interferon-stimulated gene 15) functions through covalent attachment of its protein product to target proteins or as a secreted immunomodulator. ISG15 plays a pivotal role in antiviral immunity and cellular stress responses via ISGylation. In this review, we present an integrative structural and evolutionary analysis of ISG15 and its conjugation/deconjugation machinery, highlighting key steps of the molecular basis of ISG15 and its function. Comparative analysis of Ubiquitin and Ubiquitin-like proteins reveals the evolutionary emergence of ISG15 as a distinct modifier. Structural modeling and visualization of ISG15 elucidates its enzymatic activation via the E1 enzyme UBA7 and its conjugation through the E2 enzyme UBCH8 and E3 ligase HERC5. Cryo-EM and modeled complexes provide detailed views of domain interactions and catalytic interfaces essential for ISG15 transfer. Furthermore, we identify flexible regions in the Ubiquitin-Fold Domains (UFD) of various E1 enzymes that may underlie substrate specificity. The interaction between ISG15 and its specific protease USP18, revealing conformational changes upon substrate binding that are likely critical for de-ISGylation. Together, our findings offer a comprehensive structural framework for understanding ISGylation, paving the way for targeted therapeutic strategies in immune modulation.