NikR repressor: high-affinity nickel binding to the C-terminal domain regulates binding to operator DNA

Chem Biol. 2002 Oct;9(10):1141-8. doi: 10.1016/s1074-5521(02)00241-7.


E. coli NikR repressor binds operator DNA in a nickel-dependent fashion. The pM affinity of NikR for nickel is mediated by its C-terminal 86 residues. Nickel binding induced additional secondary structure, decreased the compactness, and increased the stability of NikR. Tetramer formation by the C-terminal domain and intact NikR did not require nickel. High-affinity nickel binding decreased the NikR concentration needed to half maximally protect operator DNA from undetectable levels to 30 nM. The intracellular concentration of NikR in E. coli is high enough that saturation of the high-affinity nickel sites should lead to substantial occupancy of the nik operator. Nickel binding to a set of low-affinity NikR sites resulted in an additional large increase in operator affinity and substantially increased the size of the NikR footprint on the operator.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Circular Dichroism
  • DNA Footprinting
  • DNA, Bacterial / metabolism*
  • DNA-Binding Proteins / metabolism*
  • Escherichia coli / chemistry
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Escherichia coli Proteins*
  • Kinetics
  • Models, Genetic
  • Nickel / chemistry
  • Nickel / metabolism*
  • Operon / physiology*
  • Protein Binding
  • Protein Denaturation
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Repressor Proteins / chemistry
  • Repressor Proteins / genetics
  • Repressor Proteins / metabolism*
  • Spectrophotometry, Ultraviolet
  • Ultracentrifugation / methods
  • Urea / pharmacology


  • DNA, Bacterial
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • NikR protein, E coli
  • Repressor Proteins
  • Nickel
  • Urea