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Structure paper

TitleStructural basis of colibactin activation by the ClbP peptidase.
Journal, issue, pagesNat Chem Biol, Vol. 19, Issue 2, Page 151-158, Year 2023
Publish dateOct 17, 2022
AuthorsJosé A Velilla / Matthew R Volpe / Grace E Kenney / Richard M Walsh / Emily P Balskus / Rachelle Gaudet /
PubMed AbstractColibactin, 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 ...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.
External linksNat Chem Biol / PubMed:36253550 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.3 - 3.73 Å
Structure data

26593

7ul6

EMDB-26593, PDB-7ul6:
CryoEM structure of full-length dimeric ClbP
Method: EM (single particle) / Resolution: 3.73 Å

PDB-7mde:
Full-length S95A ClbP
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-7mdf:
Full-length S95A ClbP bound to N-acyl-D-asparagine analog
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

Chemicals

ChemComp-OLC:
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate

ChemComp-2PE:
NONAETHYLENE GLYCOL / precipitant*YM

ChemComp-IMD:
IMIDAZOLE

ChemComp-DMS:
DIMETHYL SULFOXIDE / DMSO, precipitant*YM

ChemComp-SO4:
SULFATE ION

ChemComp-CL:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-Z9A:
methyl N~2~-[4-(4-bromophenyl)butanoyl]-D-asparaginyl-L-alaninate

ChemComp-Z9G:
N~2~-[4-(4-bromophenyl)butanoyl]-D-asparagine

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

ChemComp-97N:
(2S)-2,3-dihydroxypropyl (9Z)-hexadec-9-enoate

Source
  • escherichia coli cft073 (bacteria)
KeywordsHYDROLASE / colibactin peptidase / S12 peptidase / HYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR complex / inner-membrane hydrolase

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