The anti-toxin ParD of plasmid RK2 consists of two structurally distinct moieties and belongs to the ribbon-helix-helix family of DNA-binding proteins

Biochem J. 2002 Jan 1;361(Pt 1):41-7. doi: 10.1042/0264-6021:3610041.

Abstract

NMR and CD spectroscopy have been used to characterize, both structurally and dynamically, the 82-amino-acid ParD protein of the post-segregational killing module of the broad-host-range plasmid RP4/RK2. ParD occurs as a dimer in solution and exercises two different control functions; an autoregulatory function by binding to its own promoter P(parDE) and a plasmid-stabilizing function by inhibiting ParE toxicity in cells that express ParD and ParE. Analysis of the secondary structure based on the chemical-shift indices, sequential nuclear Overhauser enhancements (NOEs) and (3)J(Halpha-NH) scalar coupling constants showed that the N-terminal domain of ParD consists of a short beta-ribbon followed by three alpha-helices, demonstrating that ParD contains a ribbon-helix-helix fold, a DNA-binding motif found in a family of small prokaryotic repressors. (15)N longitudinal (T(1)) and transverse (T(2)) relaxation measurements and hetero nuclear NOEs showed that ParD is divided into two separate domains, a well-ordered N-terminal domain and a very flexible C-terminal domain. An increase in secondary structure was observed upon addition of trifluoroethanol, suggested to result from the formation of structured stretches in the C-terminal part of the protein. This is the first experimental evidence that the DNA-binding domain of ParD belongs to the ribbon-helix-helix fold family, and this structural motif is proposed to be present in functionally similar antidote proteins.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Circular Dichroism
  • DNA Topoisomerase IV / chemistry
  • DNA Topoisomerase IV / genetics
  • DNA Topoisomerase IV / metabolism
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism*
  • Magnetic Resonance Spectroscopy
  • Molecular Sequence Data
  • Plasmids / chemistry
  • Plasmids / genetics
  • Plasmids / metabolism*
  • Protein Structure, Secondary / drug effects
  • Protein Structure, Tertiary
  • Sequence Homology, Amino Acid
  • Trifluoroethanol / pharmacology

Substances

  • Bacterial Proteins
  • DNA-Binding Proteins
  • ParD protein, Plasmid RK2
  • parD protein, Bacteria
  • Trifluoroethanol
  • DNA Topoisomerase IV