Architecture of the 99 bp DNA-six-protein regulatory complex of the lambda att site

Mol Cell. 2006 Nov 17;24(4):569-80. doi: 10.1016/j.molcel.2006.10.006.


The highly directional and tightly regulated recombination reaction used to site-specifically excise the bacteriophage lambda chromosome out of its E. coli host chromosome requires the binding of six sequence-specific proteins to a 99 bp segment of the phage att site. To gain structural insights into this recombination pathway, we measured 27 FRET distances between eight points on the 99 bp regulatory DNA bound with all six proteins. Triangulation of these distances using a metric matrix distance-geometry algorithm provided coordinates for these eight points. The resulting path for the protein-bound regulatory DNA, which fits well with the genetics, biochemistry, and X-ray crystal structures describing the individual proteins and their interactions with DNA, provides a new structural perspective into the molecular mechanism and regulation of the recombination reaction and illustrates a design by which different families of higher-order complexes can be assembled from different numbers and combinations of the same few proteins.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Attachment Sites, Microbiological / genetics*
  • Bacteriophage lambda
  • Base Sequence
  • Crystallography, X-Ray
  • DNA Nucleotidyltransferases / chemistry
  • DNA, Bacterial / chemistry*
  • DNA-Binding Proteins / chemistry*
  • Escherichia coli Proteins / chemistry
  • Factor For Inversion Stimulation Protein
  • Fluorescence Resonance Energy Transfer
  • Integrases / chemistry*
  • Integrases / physiology
  • Models, Molecular
  • Molecular Sequence Data
  • Recombination, Genetic*
  • Transcription Factors / chemistry
  • Viral Proteins / chemistry


  • DNA, Bacterial
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • Factor For Inversion Stimulation Protein
  • Fis protein, E coli
  • Transcription Factors
  • Viral Proteins
  • DNA Nucleotidyltransferases
  • Integrases
  • excisionase