1D5Y

CRYSTAL STRUCTURE OF THE E. COLI ROB TRANSCRIPTION FACTOR IN COMPLEX WITH DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.254 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA.

Kwon, H.J.Bennik, M.H.Demple, B.Ellenberger, T.

(2000) Nat.Struct.Mol.Biol. 7: 424-430

  • DOI: 10.1038/75213

  • PubMed Abstract: 
  • The Escherichia coli Rob protein is a transcription factor belonging to the AraC/XylS protein family that regulates genes involved in resistance to antibiotics, organic solvents and heavy metals. The genes encoding these proteins are activated by the ...

    The Escherichia coli Rob protein is a transcription factor belonging to the AraC/XylS protein family that regulates genes involved in resistance to antibiotics, organic solvents and heavy metals. The genes encoding these proteins are activated by the homologous proteins MarA and SoxS, although the level of activation can vary for the different transcription factors. Here we report a 2.7 A crystal structure of Rob in complex with the micF promoter that reveals an unusual mode of binding to DNA. The Rob-DNA complex differs from the previously reported structure of MarA bound to the mar promoter, in that only one of Rob's dual helix-turn-helix (HTH) motifs engages the major groove of the binding site. Biochemical studies show that sequence specific interactions involving only one of Rob's HTH motifs are sufficient for high affinity binding to DNA. The two different modes of DNA binding seen in crystal structures of Rob and MarA also match the distinctive patterns of DNA protection by AraC at several sites within the pBAD promoter. These and other findings suggest that gene activation by AraC/XylS transcription factors might involve two alternative modes of binding to DNA in different promoter contexts.


    Organizational Affiliation

    Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ROB TRANSCRIPTION FACTOR
A, D, C, B
292Escherichia coli (strain K12)Gene Names: rob
Find proteins for P0ACI0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ACI0
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*AP*CP*AP*GP*CP*AP*CP*TP*GP*AP*AP*TP*GP*TP*CP*AP*AP*AP*G)-3')M,O21N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*CP*TP*TP*TP*GP*AP*CP*AP*TP*TP*CP*AP*GP*TP*GP*CP*TP*GP*TP*C)-3')N,P21N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.254 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 75.384α = 90.00
b = 208.012β = 90.00
c = 67.731γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-04-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance