Structural basis of colibactin activation by the ClbP peptidase

Velilla, José A.; Volpe, Matthew R.; Kenney, Grace E.; Walsh, Richard M.; Balskus, Emily P.; Gaudet, Rachelle

doi:10.1038/s41589-022-01142-z

Structural basis of colibactin activation by the ClbP peptidase

Journal Article · 17 October 2022 · Nature Chemical Biology

DOI:https://doi.org/10.1038/s41589-022-01142-z· OSTI ID:2423638

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Abstract

Colibactin, a DNA cross-linking agent produced by gut bacteria, is implicated in colorectal cancer. Its biosynthesis uses a prodrug resistance mechanism: a non-toxic precursor assembled in the cytoplasm is activated after export to the periplasm. This activation is mediated by ClbP, an inner-membrane peptidase with an N-terminal periplasmic catalytic domain and a C-terminal three-helix transmembrane domain. Although the transmembrane domain is required for colibactin activation, its role in catalysis is unclear. Our structure of full-length ClbP bound to a product analog reveals an interdomain interface important for substrate binding and enzyme stability and interactions that explain the selectivity of ClbP for theN-acyl-d-asparagine prodrug motif. Based on structural and biochemical evidence, we propose that ClbP dimerizes to form an extended substrate-binding site that can accommodate a pseudodimeric precolibactin with its two terminal prodrug motifs in the two ClbP active sites, thus enabling the coordinated activation of both electrophilic warheads.

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC02-06CH11357

OSTI ID:: 2423638

Journal Information:: Nature Chemical Biology, Journal Name: Nature Chemical Biology Journal Issue: 2 Vol. 19; ISSN 1552-4450

Publisher:: Nature Publishing Group

Country of Publication:: United States

Language:: English

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