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TitleStructural study on human microbiome-derived polyketide synthases that assemble genotoxic colibactin.
Journal, issue, pagesStructure, Vol. 33, Issue 7, Page 1208-11223.e5, Year 2025
Publish dateJul 3, 2025
AuthorsMinjae Kim / Jinwoo Kim / Gyu Sung Lee / Paul Dominic B Olinares / Yougant Airan / Jasmine L Chow / Jongseok Park / Yujin Jeong / Jiho Park / Brian T Chait / Seth B Herzon / Chung Sub Kim / Jin Young Kang /
PubMed AbstractColibactin, a human microbiome-derived genotoxin, promotes colorectal cancer by damaging the host gut epithelial genomes. While colibactin is synthesized via a hybrid non-ribosomal peptide synthetase ...Colibactin, a human microbiome-derived genotoxin, promotes colorectal cancer by damaging the host gut epithelial genomes. While colibactin is synthesized via a hybrid non-ribosomal peptide synthetase (NRPS)-polyketide synthase (PKS) pathway, known as pks or clb, the structural details of its biosynthetic enzymes remain limited, hindering our understanding of its biosynthesis and clinical application. In this study, we report the cryo-EM structures of two colibactin-producing PKS enzymes, ClbC and ClbI, captured in different reaction states using a substrate-mimic crosslinker. Our structural analysis revealed the binding sites of carrier protein (CP) domains of the ClbC and ClbI on their ketosynthase (KS) domains. Further, we identified a novel NRPS-PKS docking interaction between ClbI and its upstream enzyme, ClbH, mediated by the C-terminal peptide ClbH and the dimeric interface of ClbI, establishing a 1:2 stoichiometry. These findings advance our understanding of colibactin assembly line and provide broader insights into NRPS-PKS natural product biosynthesis mechanisms.
External linksStructure / PubMed:40381618
MethodsEM (single particle)
Resolution2.91 - 3.9 Å
Structure data

38222

8xbl

EMDB-38222, PDB-8xbl:
Cryo-EM structure of colibactin assembly line polyketide synthase ClbC (apo state)
Method: EM (single particle) / Resolution: 3.06 Å

38405

8xjt

EMDB-38405, PDB-8xjt:
Cryo-EM structure of colibactin assembly line polyketide synthase ClbC (ACP-bound state)
Method: EM (single particle) / Resolution: 3.9 Å

38406

8xju

EMDB-38406, PDB-8xju:
Cryo-EM structure of colibactin assembly line polyketide synthase ClbI (apo state)
Method: EM (single particle) / Resolution: 2.91 Å

38410

8xjy

EMDB-38410, PDB-8xjy:
Cryo-EM structure of colibactin assembly line polyketide synthase ClbI KS-AT didomain crosslinked with ClbI ACP
Method: EM (single particle) / Resolution: 3.29 Å

38411

8xjz

EMDB-38411, PDB-8xjz:
Cryo-EM structure of colibactin assembly line polyketide synthase ClbI KS-AT didomain crosslinked with its precursor module, ClbH
Method: EM (single particle) / Resolution: 3.67 Å

Source
  • escherichia coli (E. coli)
KeywordsBIOSYNTHETIC PROTEIN / colibactin / microbiome / polyketide synthase / colorectal cancer / NRPS-PKS hybrid / TRANSFERASE

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