DepoCatalog: mapping diversity of 129 recombinantly produced Klebsiella phage depolymerases
Our understanding of how depolymerase sequence and structure determine substrate specificity is fragmentary due to the limited number of experimentally characterized enzymes. Here we show DepoCatalog - an experimentally validated collection of 129 recombinantly prepared Klebsiella phage depolymerases (90 enzymes produced in this study and 39 homologs from the literature), with specificity spanning 75 KL-types. Enzymes originated from podo-, sipho-, myo-, jumbo phages, and prophages. Using activity profiling, structural modeling, and domain dissection, we propose a five‑class framework that captures the architectural and functional diversity of these enzymes. DepoCatalog uncovers cross-reactivity and taxa‑specific enzymes. Structural comparisons indicate that specificity switching or extension is associated with modifications to the C‑terminal domain. We further hypothesize that podoviruses encoding up to two RBPs show greater receptor adaptability than jumbo phages with multiple specialized RBPs. Finally, we develop a publicly accessible, DepoCat dataset (https://depocat.uwr.edu.pl) for specificity, structural classification and comparison of newly identified depolymerases.
Authors
- Grażyna Majkowska-Skrobek (ORCID: https://orcid.org/0000-0002-7901-619X)
- Aleksandra Otwinowska (ORCID: https://orcid.org/0000-0002-3911-5409)
- Flavia Squeglia (ORCID: https://orcid.org/0000-0001-9142-3313)
- Sabrina Green
- Jana Stender
- Rafal Mostowy (ORCID: https://orcid.org/0000-0002-4557-3748)
- Barbara Maciejewska (ORCID: https://orcid.org/0000-0002-4876-8743)
- Sebastian Olejniczak (ORCID: https://orcid.org/0000-0003-1523-788X)
- Janusz Koszucki (ORCID: https://orcid.org/0000-0002-1766-5637)
- Régis Tournebize (ORCID: https://orcid.org/0000-0003-3000-6801)
- Vyshakh R. Panicker
- Maria Pozniak (ORCID: https://orcid.org/0009-0002-4589-0222)
- Mathilde Hulsens (ORCID: https://orcid.org/0000-0002-0662-8144)
- Maha Niazi
- Rob Lavigne (ORCID: https://orcid.org/0000-0001-7377-1314)
- Jens A. Hammerl (ORCID: https://orcid.org/0000-0002-6930-4358)
- Yves Briers (ORCID: https://orcid.org/0000-0001-7723-1040)
- Sara Jablonska (ORCID: https://orcid.org/0009-0009-3651-6782)
- Stan J. J. Brouns
- Rita Berisio
- Zuzanna Drulis-Kawa (ORCID: https://orcid.org/0000-0002-4733-4660)
- Joachim J. Bugert
- Agnieszka Latka (ORCID: https://orcid.org/0000-0003-4492-497X)
Institutions
- Jagiellonian University (PL)
- Inserm (FR)
- Institut Pasteur (FR)
- University of Wrocław (PL)
- Federal Institute for Risk Assessment (DE)
- Ghent University (BE)
- Sorbonne Université (FR)
- Universität der Bundeswehr München (DE)
- Centre d'Immunologie et des Maladies Infectieuses (FR)
- Institute of Biostructure and Bioimaging (IT)
- Institut für Mikrobiologie der Bundeswehr
- Delft University of Technology (NL)
- KU Leuven (BE)
Publication Details
- Journal
- Nature Communications
- Published
- 2026-05-22
- DOI
- https://doi.org/10.1038/s41467-026-73570-7
- Primary Topic
- Bacteriophages and microbial interactions
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Joint Programming Initiative on Antimicrobial Resistance
- Agence Nationale de la Recherche
- Monash University
- Bundesministerium für Bildung und Forschung
- Fonds Wetenschappelijk Onderzoek
- Narodowe Centrum Nauki
- Vlaamse regering
- Narodowa Agencja Wymiany Akademickiej