8CJH | pdb_00008cjh

Architecture of a PKS-NRPS hybrid megaenzyme involved in the biosynthesis of the genotoxin colibactin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 
    0.238 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.217 (DCC) 

Starting Model: in silico
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This is version 1.2 of the entry. See complete history. 

Literature

Architecture of a PKS-NRPS hybrid megaenzyme involved in the biosynthesis of the genotoxin colibactin.

Bonhomme, S., Contreras-Martel, C., Dessen, A., Macheboeuf, P.

(2023) Structure 31: 700

  • DOI: https://doi.org/10.1016/j.str.2023.03.012
  • Primary Citation Related Structures: 
    8CJH

  • PubMed Abstract: 

    The genotoxin colibactin produced by Escherichia coli is involved in the development of colorectal cancers. This secondary metabolite is synthesized by a multi-protein machinery, mainly composed of non-ribosomal peptide synthetase (NRPS)/polyketide synthase (PKS) enzymes. In order to decipher the function of a PKS-NRPS hybrid enzyme implicated in a key step of colibactin biosynthesis, we conducted an extensive structural characterization of the ClbK megaenzyme. Here we present the crystal structure of the complete trans-AT PKS module of ClbK showing structural specificities of hybrid enzymes. In addition, we report the SAXS solution structure of the full-length ClbK hybrid that reveals a dimeric organization as well as several catalytic chambers. These results provide a structural framework for the transfer of a colibactin precursor through a PKS-NRPS hybrid enzyme and can pave the way for re-engineering PKS-NRPS hybrid megaenzymes to generate diverse metabolites with many applications.

    • Organizational Affiliation: 
    • University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Bacterial Pathogenesis Group, 38000 Grenoble, France.

Macromolecule Content 

  • Total Structure Weight: 512.58 kDa 
  • Atom Count: 22,022 
  • Modeled Residue Count: 2,892 
  • Deposited Residue Count: 4,722 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Colibactin hybrid non-ribosomal peptide synthetase/type I polyketide synthase ClbK
A, B, C, D, E
A, B, C, D, E, F
787Escherichia coliMutation(s): 0 
Gene Names: clbK, E4T84_20075
UniProt
Find proteins for Q0P7K1 (Escherichia coli)
Explore Q0P7K1 
Go to UniProtKB:  Q0P7K1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0P7K1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free:  0.238 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.217 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 187.643α = 90
b = 233.374β = 90
c = 256.598γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other governmentFranceM32917
Other governmentFranceAO12-20

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Database references, Refinement description
  • Version 1.2: 2024-06-19
    Changes: Data collection, Refinement description