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Structural basis of the amidase ClbL central to the biosynthesis of the genotoxin colibactin
Colibactin is a genotoxic natural product produced by select commensal bacteria in the human gut microbiota. The compound is a bis-electrophile that is predicted to form interstrand DNA cross-links in target cells, leading to double-strand DNA breaks. The biosynthesis of colibactin is carried out by...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2023
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10478638/ https://www.ncbi.nlm.nih.gov/pubmed/37561403 http://dx.doi.org/10.1107/S2059798323005703 |
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author | Tripathi, Prabhanshu Mousa, Jarrod J. Guntaka, Naga Sandhya Bruner, Steven D. |
author_facet | Tripathi, Prabhanshu Mousa, Jarrod J. Guntaka, Naga Sandhya Bruner, Steven D. |
author_sort | Tripathi, Prabhanshu |
collection | PubMed |
description | Colibactin is a genotoxic natural product produced by select commensal bacteria in the human gut microbiota. The compound is a bis-electrophile that is predicted to form interstrand DNA cross-links in target cells, leading to double-strand DNA breaks. The biosynthesis of colibactin is carried out by a mixed NRPS–PKS assembly line with several noncanonical features. An amidase, ClbL, plays a key role in the pathway, catalyzing the final step in the formation of the pseudodimeric scaffold. ClbL couples α-aminoketone and β-ketothioester intermediates attached to separate carrier domains on the NRPS–PKS assembly. Here, the 1.9 Å resolution structure of ClbL is reported, providing a structural basis for this key step in the colibactin biosynthetic pathway. The structure reveals an open hydrophobic active site surrounded by flexible loops, and comparison with homologous amidases supports its unusual function and predicts macromolecular interactions with pathway carrier-protein substrates. Modeling protein–protein interactions supports a predicted molecular basis for enzyme–carrier domain interactions. Overall, the work provides structural insight into this unique enzyme that is central to the biosynthesis of colibactin. |
format | Online Article Text |
id | pubmed-10478638 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
spelling | pubmed-104786382023-09-06 Structural basis of the amidase ClbL central to the biosynthesis of the genotoxin colibactin Tripathi, Prabhanshu Mousa, Jarrod J. Guntaka, Naga Sandhya Bruner, Steven D. Acta Crystallogr D Struct Biol Research Papers Colibactin is a genotoxic natural product produced by select commensal bacteria in the human gut microbiota. The compound is a bis-electrophile that is predicted to form interstrand DNA cross-links in target cells, leading to double-strand DNA breaks. The biosynthesis of colibactin is carried out by a mixed NRPS–PKS assembly line with several noncanonical features. An amidase, ClbL, plays a key role in the pathway, catalyzing the final step in the formation of the pseudodimeric scaffold. ClbL couples α-aminoketone and β-ketothioester intermediates attached to separate carrier domains on the NRPS–PKS assembly. Here, the 1.9 Å resolution structure of ClbL is reported, providing a structural basis for this key step in the colibactin biosynthetic pathway. The structure reveals an open hydrophobic active site surrounded by flexible loops, and comparison with homologous amidases supports its unusual function and predicts macromolecular interactions with pathway carrier-protein substrates. Modeling protein–protein interactions supports a predicted molecular basis for enzyme–carrier domain interactions. Overall, the work provides structural insight into this unique enzyme that is central to the biosynthesis of colibactin. International Union of Crystallography 2023-08-10 /pmc/articles/PMC10478638/ /pubmed/37561403 http://dx.doi.org/10.1107/S2059798323005703 Text en © Prabhanshu Tripathi et al. 2023 https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited. |
spellingShingle | Research Papers Tripathi, Prabhanshu Mousa, Jarrod J. Guntaka, Naga Sandhya Bruner, Steven D. Structural basis of the amidase ClbL central to the biosynthesis of the genotoxin colibactin |
title | Structural basis of the amidase ClbL central to the biosynthesis of the genotoxin colibactin |
title_full | Structural basis of the amidase ClbL central to the biosynthesis of the genotoxin colibactin |
title_fullStr | Structural basis of the amidase ClbL central to the biosynthesis of the genotoxin colibactin |
title_full_unstemmed | Structural basis of the amidase ClbL central to the biosynthesis of the genotoxin colibactin |
title_short | Structural basis of the amidase ClbL central to the biosynthesis of the genotoxin colibactin |
title_sort | structural basis of the amidase clbl central to the biosynthesis of the genotoxin colibactin |
topic | Research Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10478638/ https://www.ncbi.nlm.nih.gov/pubmed/37561403 http://dx.doi.org/10.1107/S2059798323005703 |
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