5D4R

Crystal Structure of AraR(DBD) in complex with operator ORE1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Plasticity in Repressor-DNA Interactions Neutralizes Loss of Symmetry in Bipartite Operators.

Jain, D.Narayanan, N.Nair, D.T.

(2016) J.Biol.Chem. 291: 1235-1242

  • DOI: 10.1074/jbc.M115.689695
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Transcription factor-DNA interactions are central to gene regulation. Many transcription factors regulate multiple target genes and can bind sequences that do not conform strictly to the consensus. To understand the structural mechanism utilized by t ...

    Transcription factor-DNA interactions are central to gene regulation. Many transcription factors regulate multiple target genes and can bind sequences that do not conform strictly to the consensus. To understand the structural mechanism utilized by the transcription regulators to bind diverse target sequences, we have employed the repressor AraR from Bacillus subtilis as a model system. AraR is known to bind to eight different operator sites in the bacterial genome. Although there are differences in the sequences of four of these operators, ORE1, ORX1, ORA1, and ORR3, the AraR-DNA binding domain (AraR-DBD) as well as full-length AraR unexpectedly binds to each of these sequences with similar affinities as measured by fluorescence anisotropy experiments. We have determined crystal structures of AraR-DBD in complex with two different natural operators ORE1 and ORX1 up to 2.07 and 1.97 Å resolution, respectively. These structures were compared with the previously reported structures of AraR-DBD bound to two other natural operators (ORA1 and ORR3). Interactions of two molecules of AraR-DBD with the symmetric operator, ORE1, are identical, but their interaction with the non-symmetric operator ORX1 results in breakdown of the symmetry in protein-DNA interactions. The novel interactions observed are accompanied by local conformational change in the DNA. ChIP-sequencing (ChIP-Seq) data on other transcription factors has shown that they can bind to diverse targets, and hence the plasticity exhibited by AraR may be a general phenomenon. The ability of transcription factors to form alternate interactions may be important for employment in new functions and evolution of novel regulatory circuits.


    Organizational Affiliation

    From the Transcription Regulation Lab and the National Centre for Biological Sciences (NCBS-TIFR), UAS-GKVK Campus, Bellary Road, Bangalore 560065, and deepti@rcb.res.in.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Arabinose metabolism transcriptional repressor
A, B
88Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: araR (araC, yvbS)
Find proteins for P96711 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P96711
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*TP*AP*AP*TP*TP*AP*GP*TP*AP*CP*GP*TP*AP*CP*AP*AP*AP*TP*A)-3')T21synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*TP*AP*TP*TP*TP*GP*TP*AP*CP*GP*TP*AP*CP*TP*AP*AP*TP*TP*AP*T)-3')U21synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 134.081α = 90.00
b = 42.433β = 114.82
c = 67.232γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
India--

Revision History 

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2016-01-27
    Type: Database references, Derived calculations