Crystal Structure of IclR Family Transcriptional Regulator from Brucella abortus

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report

This is version 2.2 of the entry. See complete history


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: https://doi.org/10.1074/jbc.RA118.002045
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    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

    Departments of Biochemistry and Molecular Biology, Chicago, Illinois 60637; Howard Taylor Ricketts Laboratory, University of Chicago, Argonne, Illinois 60439.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IclR family transcriptional regulator
A, B, C, D
267Brucella abortusMutation(s): 0 
Gene Names: BFJ58_02720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on EDO

Download Ideal Coordinates CCD File 
I [auth C]1,2-ETHANEDIOL
C2 H6 O2
Query on ACY

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth B]
J [auth C]
K [auth C]
E [auth A],
F [auth A],
H [auth B],
J [auth C],
K [auth C],
L [auth D],
M [auth D]
C2 H4 O2
Query on CA

Download Ideal Coordinates CCD File 
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B, C, D
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.152α = 90
b = 112.462β = 115.86
c = 83.649γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI107792
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI107159

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence
  • Version 2.0: 2017-10-25
    Changes: Advisory, Atomic model, Database references, Derived calculations
  • Version 2.1: 2018-12-19
    Changes: Data collection, Database references
  • Version 2.2: 2019-11-27
    Changes: Author supporting evidence