7MDF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.191 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Structural basis of colibactin activation by the ClbP peptidase.

Velilla, J.A.Volpe, M.R.Kenney, G.E.Walsh Jr., R.M.Balskus, E.P.Gaudet, R.

(2023) Nat Chem Biol 19: 151-158

  • DOI: https://doi.org/10.1038/s41589-022-01142-z

  • 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.


  • Organizational Affiliation

    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase480Escherichia coli CFT073Mutation(s): 3 
Gene Names: 
EC: 3.5.2.6
Membrane Entity: Yes 
UniProt
Find proteins for A0A0H2V8D3 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Explore A0A0H2V8D3 
Go to UniProtKB:  A0A0H2V8D3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2V8D3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AV0
Query on AV0

Download Ideal Coordinates CCD File 
I [auth A]Lauryl Maltose Neopentyl Glycol
C47 H88 O22
MADJBYLAYPCCOO-VWHTXWAPSA-N
Z9A
Query on Z9A

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D [auth A]methyl N~2~-[4-(4-bromophenyl)butanoyl]-D-asparaginyl-L-alaninate
C18 H24 Br N3 O5
UMJYMQGCXBKOHD-SMDDNHRTSA-N
2PE
Query on 2PE

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F [auth A],
G [auth A],
H [auth A]
NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
Z9G (Subject of Investigation/LOI)
Query on Z9G

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E [auth A]N~2~-[4-(4-bromophenyl)butanoyl]-D-asparagine
C14 H17 Br N2 O4
VRZHKETUQBKIPG-LLVKDONJSA-N
97N
Query on 97N

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J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
(2S)-2,3-dihydroxypropyl (9Z)-hexadec-9-enoate
C19 H36 O4
KVYUBFKSKZWZSV-ZEVQVBBLSA-N
SO4
Query on SO4

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O [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS
Query on DMS

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B [auth A],
C [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL
Query on CL

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P [auth A],
Q [auth A],
R [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.686α = 90
b = 96.686β = 90
c = 182.736γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM120996
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA208834

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-28
    Type: Initial release
  • Version 1.1: 2022-11-09
    Changes: Database references
  • Version 1.2: 2023-02-08
    Changes: Database references
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.4: 2023-12-13
    Changes: Derived calculations, Structure summary
  • Version 1.5: 2024-10-30
    Changes: Structure summary