8CJH

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 
  • R-Value Work: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.1 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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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: clbKE4T84_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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.217 
  • 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

View Full Validation Report



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