5TED

Effector binding domain of QuiR in complex with shikimate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 2.4 of the entry. See complete history


Literature

Shikimate Induced Transcriptional Activation of Protocatechuate Biosynthesis Genes by QuiR, a LysR-Type Transcriptional Regulator, in Listeria monocytogenes.

Prezioso, S.M.Xue, K.Leung, N.Gray-Owen, S.D.Christendat, D.

(2018) J Mol Biol 430: 1265-1283

  • DOI: https://doi.org/10.1016/j.jmb.2018.03.003
  • Primary Citation of Related Structures:  
    5TED

  • PubMed Abstract: 

    Listeria monocytogenes is a common foodborne bacterial pathogen that contaminates plant and animal consumable products. The persistent nature of L. monocytogenes is associated with millions of dollars in food recalls annually. Here, we describe the role of shikimate in directly modulating the expression of genes encoding enzymes for the conversion of quinate and shikimate metabolites to protocatechuate. In L. monocytogenes, these genes are found within two operons, named qui1 and qui2. In addition, a gene named quiR, encoding a LysR-Type Transcriptional Regulator (QuiR), is located immediately upstream of the qui1 operon. Transcriptional lacZ-promoter fusion experiments show that QuiR induces gene expression of both qui1 and qui2 operons in the presence of shikimate. Furthermore, co-crystallization of the QuiR effector binding domain in complex with shikimate provides insights into the mechanism of activation of this regulator. Together these data show that upon shikimate accumulation, QuiR activates the transcription of genes encoding enzymes involved in shikimate and quinate utilization for the production of protocatechuate. Furthermore, the accumulation of protocatechuate leads to the inhibition of Listeria growth. Since protocatechuate is not known to be utilized by Listeria, its role is distinct from those established in other bacteria.


  • Organizational Affiliation

    Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada M5S 3B2.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lmo0488 proteinA [auth B],
B [auth A]
226Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: lmo0488
UniProt
Find proteins for Q8Y9N7 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Explore Q8Y9N7 
Go to UniProtKB:  Q8Y9N7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8Y9N7
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
His Tag peptideC [auth H]9Escherichia coliMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SKM
Query on SKM

Download Ideal Coordinates CCD File 
D [auth B],
E [auth A]
(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID
C7 H10 O5
JXOHGGNKMLTUBP-HSUXUTPPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.89α = 90
b = 92.849β = 90
c = 113.915γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-2015-06747

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 2.0: 2018-03-28
    Changes: Data collection, Database references, Polymer sequence
  • Version 2.1: 2018-05-02
    Changes: Data collection, Database references
  • Version 2.2: 2020-01-08
    Changes: Author supporting evidence
  • Version 2.3: 2024-03-06
    Changes: Data collection, Database references
  • Version 2.4: 2024-04-03
    Changes: Refinement description