7MDF image
Entry Detail
PDB ID:
7MDF
Title:
Full-length S95A ClbP bound to N-acyl-D-asparagine analog
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2021-04-04
Release Date:
2022-09-28
Method Details:
Experimental Method:
Resolution:
2.30 Å
R-Value Free:
0.21
R-Value Work:
0.19
Space Group:
P 42 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Beta-lactamase
Mutations:S95A, L454M, I478M
Chain IDs:A
Chain Length:480
Number of Molecules:1
Biological Source:Escherichia coli CFT073
Primary Citation
Structural basis of colibactin activation by the ClbP peptidase.
Nat.Chem.Biol. 19 151 158 (2023)
PMID: 36253550 DOI: 10.1038/s41589-022-01142-z

Abstact

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 the N-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.

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