5UGZ | pdb_00005ugz

Crystal structure of ClbQ from the colibactin NRPS/PKS pathway

• PDB DOI: https://doi.org/10.2210/pdb5UGZ/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-01-10 Released: 2017-09-20 
• Deposition Author(s): Guntaka, N.S., Bruner, S.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.208 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Structure and Functional Analysis of ClbQ, an Unusual Intermediate-Releasing Thioesterase from the Colibactin Biosynthetic Pathway.

Guntaka, N.S., Healy, A.R., Crawford, J.M., Herzon, S.B., Bruner, S.D.

(2017) ACS Chem Biol 12: 2598-2608

• PubMed: 28846367 
• DOI: https://doi.org/10.1021/acschembio.7b00479
• Primary Citation Related Structures: 
  5UGZ


• PubMed Abstract: 
  

  Colibactin is a genotoxic hybrid nonribosomal peptide/polyketide secondary metabolite produced by various pathogenic and probiotic bacteria residing in the human gut. The presence of colibactin metabolites has been correlated to colorectal cancer formation in several studies. The specific function of many gene products in the colibactin gene cluster can be predicted. However, the role of ClbQ, a type II editing thioesterase, has not been established. The importance of ClbQ has been demonstrated by genetic deletions that abolish colibactin cytotoxic activity, and recent studies suggest an atypical role in releasing pathway intermediates from the assembly line. Here we report the 2.0 Å crystal structure and biochemical characterization of ClbQ. Our data reveal that ClbQ exhibits greater catalytic efficiency toward acyl-thioester substrates as compared to precolibactin intermediates and does not discriminate among carrier proteins. Cyclized pyridone-containing colibactins, which are off-pathway derivatives, are not viable substrates for ClbQ, while linear precursors are, supporting a role of ClbQ in facilitating the promiscuous off-loading of premature precolibactin metabolites and novel insights into colibactin biosynthesis.

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Organizational Affiliation: 
• Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States.
Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.
Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States.
Department of Microbial Pathogenesis, Yale School of Medicine , New Haven, Connecticut 06536, United States.
Department of Pharmacology, Yale School of Medicine , New Haven, Connecticut 06520, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.23 kDa 
• Atom Count: 4,067 
• Modeled Residue Count: 478 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative thioesterase	A, B	260	Escherichia coli	Mutation(s): 0  Gene Names: clbQ EC: 1.1
UniProt
Find proteins for Q0P7K7 (Escherichia coli) Explore Q0P7K7  Go to UniProtKB:  Q0P7K7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BME	C [auth A], D [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.208 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.971	α = 90
b = 94.994	β = 109.18
c = 68.444	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-20 
Deposition Author(s): Guntaka, N.S., Bruner, S.D.

Revision History  

• Version 1.0: 2017-09-20
  Type: Initial release
  
• Version 1.1: 2017-11-01
  Changes: Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description