4H0E

Crystal Structure of mutant ORR3 in complex with NTD of AraR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.973 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Spacing between core recognition motifs determines relative orientation of AraR monomers on bipartite operators.

Jain, D.Nair, D.T.

(2013) Nucleic Acids Res. 41: 639-647

  • DOI: 10.1093/nar/gks962
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Transcription factors modulate expression primarily through specific recognition of cognate sequences resident in the promoter region of target genes. AraR (Bacillus subtilis) is a repressor of genes involved in L-arabinose metabolism. It binds to ei ...

    Transcription factors modulate expression primarily through specific recognition of cognate sequences resident in the promoter region of target genes. AraR (Bacillus subtilis) is a repressor of genes involved in L-arabinose metabolism. It binds to eight different operators present in five different promoters with distinct affinities through a DNA binding domain at the N-terminus. The structures of AraR-NTD in complex with two distinct operators (ORA1 and ORR3) reveal that two monomers bind to one recognition motif (T/ANG) each in the bipartite operators. The structures show that the two recognition motifs are spaced apart by six bases in cases of ORA1 and eight bases in case of ORR3. This increase in the spacing in the operators by two base pairs results in a drastic change in the position and orientation of the second monomer on DNA in the case of ORR3 when compared with ORA1. Because AraR binds to the two operators with distinct affinities to achieve different levels of repression, this observation suggests that the variation in the spacing between core recognition motifs could be a strategy used by this transcription modulator to differentially influence gene expression.


    Organizational Affiliation

    Laboratory 4, National Centre for Biological Sciences, NCBS-TIFR, UAS-GKVK Campus, Bellary Road, Bangalore, Karnataka 560065, India.




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
5'-D(*AP*AP*AP*TP*TP*TP*GP*TP*CP*CP*GP*TP*AP*CP*AP*TP*TP*TP*TP*AP*T)-3'U21N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*TP*AP*TP*AP*AP*AP*AP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*AP*AP*TP*T)-3'T21N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
B, T, U
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
T
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.973 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.219 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 137.800α = 90.00
b = 42.620β = 114.92
c = 67.440γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PXIIIdata collection
XDSdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2012-09-08 
  • Released Date: 2013-02-06 
  • Deposition Author(s): Nair, D.T., Jain, D.

Revision History 

  • Version 1.0: 2013-02-06
    Type: Initial release