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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...

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Autores principales: Tripathi, Prabhanshu, Mousa, Jarrod J., Guntaka, Naga Sandhya, Bruner, Steven D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2023
Materias:
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.
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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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