ArticleScientific reports2016
Structural studies of the yeast DNA damage-inducible protein Ddi1 reveal domain architecture of this eukaryotic protein family.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 50 citations in OpenAlex.
- K48-ubiquitin-dependent proteases cut-up post-ER proteins.Nature communications · 2026Article
- Malaria parasites require a divergent heme oxygenase for apicoplast gene expression and biogenesis.eLife · 2024Article
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- Malaria parasites require a divergent heme oxygenase for apicoplast gene expression and biogenesis.bioRxiv : the preprint server for biology · 2024Article
- From the TOP: Formation, recognition and resolution of topoisomerase DNA protein crosslinks.DNA repair · 2024Review
- The human retroviral-like aspartic protease 1 (ASPRV1): From in vitro studies to clinical correlations.The Journal of biological chemistry · 2024Review
- Unveiling the molecular mechanisms of the type IX secretion system's response regulator: Structural and functional insights.PNAS nexus · 2024Article
- Structural Catalytic Core of the Members of the Superfamily of Acid Proteases.Molecules (Basel, Switzerland) · 2024Review
- Domains in Action: Understanding Ddi1's Diverse Functions in the Ubiquitin-Proteasome System.International journal of molecular sciences · 2024Review
- Aldehyde-induced DNA-protein crosslinks- DNA damage, repair and mutagenesis.Frontiers in oncology · 2024Review
- Structural and functional insights into the DNA damage-inducible protein 1 (Ddi1) from protozoa.Current research in structural biology · 2022Article
- The STI1-domain is a flexible alpha-helical fold with a hydrophobic groove.Protein science : a publication of the Protein Society · 2021Article
- Emerging roles of Wss1 in the survival of Candida albicans under genotoxic stresses.Current genetics · 2021Review
- DNA-protein crosslink proteases in genome stability.Communications biology · 2021Review
- Ddi1 is a ubiquitin-dependent protease.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Functional Study of the Retrotransposon-Derived Human PEG10 Protease.International journal of molecular sciences · 2020Article
- Dimer Interface Organization is a Main Determinant of Intermonomeric Interactions and Correlates with Evolutionary Relationships of Retroviral and Retroviral-Like Ddi1 and Ddi2 Proteases.International journal of molecular sciences · 2020Article
- DNA-Histone Cross-Links: Formation and Repair.Frontiers in cell and developmental biology · 2020Review
- Detailed Dissection of UBE3A-Mediated DDI1 Ubiquitination.Frontiers in physiology · 2019Article
- Docking simulation between HIV peptidase inhibitors and Trypanosoma cruzi aspartyl peptidase.BMC research notes · 2018Article
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Authors and funding
13 authors at 3 institutions in 2 countries.
Funding
Abstract
The eukaryotic Ddi1 family is defined by a conserved retroviral aspartyl protease-like (RVP) domain found in association with a ubiquitin-like (UBL) domain. Ddi1 from Saccharomyces cerevisiae additionally contains a ubiquitin-associated (UBA) domain. The substrate specificity and role of the protease domain in the biological functions of the Ddi family remain unclear. Yeast Ddi1 has been implicated in the regulation of cell cycle progression, DNA-damage repair, and exocytosis. Here, we investigated the multi-domain structure of yeast Ddi1 using X-ray crystallography, nuclear magnetic resonance, and small-angle X-ray scattering. The crystal structure of the RVP domain sheds light on a putative substrate recognition site involving a conserved loop. Isothermal titration calorimetry confirms that both UBL and UBA domains bind ubiquitin, and that Ddi1 binds K48-linked diubiquitin with enhanced affinity. The solution NMR structure of a helical domain that precedes the protease displays tertiary structure similarity to DNA-binding domains from transcription regulators. Our structural studies suggest that the helical domain could serve as a landing platform for substrates in conjunction with attached ubiquitin chains binding to the UBL and UBA domains.
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