5WHM

Crystal Structure of IclR Family Transcriptional Regulator from Brucella abortus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history

Literature

Molecular control of gene expression byBrucellaBaaR, an IclR-type transcriptional repressor.

Herrou, J.Czyz, D.M.Fiebig, A.Willett, J.W.Kim, Y.Wu, R.Babnigg, G.Crosson, S.

(2018) J. Biol. Chem. 293: 7437-7456

  • DOI: 10.1074/jbc.RA118.002045

  • PubMed Abstract: 
  • The general stress response sigma factor σ <sup>E1 </sup> directly and indirectly regulates the transcription of dozens of genes that influence stress survival and host infection in the zoonotic pathogen <i>Brucella abortus </i> Characterizing the f ...

    The general stress response sigma factor σ E1 directly and indirectly regulates the transcription of dozens of genes that influence stress survival and host infection in the zoonotic pathogen Brucella abortus Characterizing the functions of σ E1 -regulated genes therefore would contribute to our understanding of B. abortus physiology and infection biology. σ E1 indirectly activates transcription of the IclR family regulator Bab2_0215, but the function of this regulator remains undefined. Here, we present a structural and functional characterization of Bab2_0215, which we have named B rucella a dipic acid- a ctivated r egulator (BaaR). We found that BaaR adopts a classic IclR-family fold and directly represses the transcription of two operons with predicted roles in carboxylic acid oxidation. BaaR binds two sites on chromosome II between baaR and a divergently transcribed hydratase/dehydrogenase ( acaD2 ), and it represses transcription of both genes. We identified three carboxylic acids (adipic acid, tetradecanedioic acid, and ϵ-aminocaproic acid) and a lactone (ϵ-caprolactone) that enhance transcription from the baaR and acaD2 promoters. However, neither the activating acids nor caprolactone enhanced transcription by binding directly to BaaR. Induction of baaR transcription by adipic acid required the gene bab2_0213 , which encodes a major facilitator superfamily transporter, suggesting that Bab2_0213 transports adipic acid across the inner membrane. We conclude that a suite of structurally related organic molecules activate transcription of genes repressed by BaaR. Our study provides molecular-level understanding of a gene expression program in B. abortus that is downstream of σ E1 .


    Organizational Affiliation

    the Argonne National Laboratory, Argonne, Illinois 60439.,Microbiology, University of Chicago, Chicago, Illinois 60637.,From the Departments of Biochemistry and Molecular Biology and.,the Howard Taylor Ricketts Laboratory, University of Chicago, Argonne, Illinois 60439, and.,From the Departments of Biochemistry and Molecular Biology and scrosson@uchicago.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IclR family transcriptional regulator
A, B, C, D
267N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
A, B, C, D
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 74.152α = 90.00
b = 112.462β = 115.86
c = 83.649γ = 90.00
Software Package:
Software NamePurpose
HKL-3000phasing
HKL-3000data scaling
HKL-3000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence
  • Version 2.0: 2017-10-25
    Type: Advisory, Atomic model, Database references, Derived calculations
  • Version 2.1: 2018-12-19
    Type: Data collection, Database references