3JSO

Classic Protein With a New Twist: crystal structure of a LexA repressor DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.266 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the LexA-DNA complex and implications for SOS box measurement.

Zhang, A.P.Pigli, Y.Z.Rice, P.A.

(2010) Nature 466: 883-886

  • DOI: 10.1038/nature09200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The eubacterial SOS system is a paradigm of cellular DNA damage and repair, and its activation can contribute to antibiotic resistance. Under normal conditions, LexA represses the transcription of many DNA repair proteins by binding to SOS 'boxes' in ...

    The eubacterial SOS system is a paradigm of cellular DNA damage and repair, and its activation can contribute to antibiotic resistance. Under normal conditions, LexA represses the transcription of many DNA repair proteins by binding to SOS 'boxes' in their operators. Under genotoxic stress, accumulating complexes of RecA, ATP and single-stranded DNA (ssDNA) activate LexA for autocleavage. To address how LexA recognizes its binding sites, we determined three crystal structures of Escherichia coli LexA in complex with SOS boxes. Here we report the structure of these LexA-DNA complexes. The DNA-binding domains of the LexA dimer interact with the DNA in the classical fashion of a winged helix-turn-helix motif. However, the wings of these two DNA-binding domains bind to the same minor groove of the DNA. These wing-wing contacts may explain why the spacing between the two half-sites of E. coli SOS boxes is invariant.


    Organizational Affiliation

    Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LexA repressor
A, B
202Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: lexA (exrA, spr, tsl, umuA)
EC: 3.4.21.88
Find proteins for P0A7C2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7C2
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*TP*AP*CP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*GP*TP*A)-3')C,D22N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.266 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 100.975α = 90.00
b = 106.935β = 90.00
c = 65.895γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
SCALEPACKdata scaling
REFMACrefinement
SOLVEphasing
DENZOdata reduction
DMphasing
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-03-21
    Type: Database references
  • Version 1.3: 2017-11-01
    Type: Refinement description