DNA binding of PhoB and its interaction with RNA polymerase

J Mol Biol. 1996 May 31;259(1):15-26. doi: 10.1006/jmbi.1996.0298.


We have identified the DNA-binding domain (DBD) of an Escherichia coli activator protein PhoB as its C-terminal 91 residues. Four amino acid positions in the PhoB DBD are found important for interaction with the RNA polymerase holoenzyme that contains the sigma 70 subunit. Assuming that the PhoB DBD is structurally similar to the histone H5 DBD, the four positions are placed around the turn region that connects two putative helices, 2 and 3 (helix 3 is likely to be the recognition helix). The binding sites of PhoB, three with the sequence TGTCA and one of TTACA, are identified in the pstS promoter. The pstS promoter has intrinsic bending (or bendability), which is much enhanced upon binding PhoB. On the basis of the above, some aspects of the PhoB-DNA-RNA polymerase interaction are discussed.

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Base Sequence
  • Binding Sites
  • Carrier Proteins / chemistry
  • Carrier Proteins / genetics
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / metabolism*
  • DNA-Directed RNA Polymerases / metabolism*
  • Electrophoresis / methods
  • Escherichia coli / chemistry
  • Escherichia coli Proteins*
  • Membrane Proteins / chemistry
  • Membrane Proteins / genetics
  • Models, Molecular
  • Molecular Sequence Data
  • Mutation
  • Nucleic Acid Conformation
  • Periplasmic Binding Proteins*
  • Phosphate-Binding Proteins
  • Promoter Regions, Genetic
  • Protein Binding
  • Protein Conformation
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Sequence Deletion
  • Sequence Homology, Amino Acid


  • Bacterial Proteins
  • Carrier Proteins
  • DNA, Bacterial
  • Escherichia coli Proteins
  • Membrane Proteins
  • Periplasmic Binding Proteins
  • Phosphate-Binding Proteins
  • PstS protein, E coli
  • Recombinant Proteins
  • PhoB protein, Bacteria
  • DNA-Directed RNA Polymerases