7MDF

Full-length S95A ClbP bound to N-acyl-D-asparagine analog

Summary for 7MDF

• Entry DOI: 10.2210/pdb7mdf/pdb
• Related: 7MDC 7MDE 7UL6
• Descriptor: Beta-lactamase, DIMETHYL SULFOXIDE, methyl N~2~-[4-(4-bromophenyl)butanoyl]-D-asparaginyl-L-alaninate, ... (10 entities in total)
• Functional Keywords: colibactin peptidase, s12 peptidase, hydrolase, hydrolase-inhibitor complex, hydrolase/inhibitor
• Biological source: Escherichia coli CFT073
• Total number of polymer chains: 1
• Total formula weight: 58040.08

Authors

Velilla, J.A.,Volpe, M.R.,Gaudet, R. (deposition date: 2021-04-04, release date: 2022-09-28, Last modification date: 2024-10-30)

Primary citation

Velilla, J.A.,Volpe, M.R.,Kenney, G.E.,Walsh Jr., R.M.,Balskus, E.P.,Gaudet, R.
Structural basis of colibactin activation by the ClbP peptidase.
Nat.Chem.Biol., 19:151-158, 2023

PubMed 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 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.

PubMed: 36253550
DOI: 10.1038/s41589-022-01142-z

Experimental method

X-RAY DIFFRACTION (2.3 Å)