Evidence for displacements of the C-helix by CO ligation and DNA binding to CooA revealed by UV resonance Raman spectroscopy

J Biol Chem. 2006 Apr 21;281(16):11271-8. doi: 10.1074/jbc.M513261200. Epub 2006 Jan 26.

Abstract

The UV and visible resonance Raman spectra are reported for CooA from Rhodospirillum rubrum, which is a transcriptional regulator activated by growth in a CO atmosphere. CO binding to heme in its sensor domain causes rearrangement of its DNA-binding domain, allowing binding of DNA with a specific sequence. The sensor and DNA-binding domains are linked by a hinge region that follows a long C-helix. UV resonance Raman bands arising from Trp-110 in the C-helix revealed local movement around Trp-110 upon CO binding. The indole side chain of Trp-110, which is exposed to solvent in the CO-free ferrous state, becomes buried in the CO-bound state with a slight change in its orientation but maintains a hydrogen bond with a water molecule at the indole nitrogen. This is the first experimental data supporting a previously proposed model involving displacement of the C-helix and heme sliding. The UV resonance Raman spectra for the CooA-DNA complex indicated that binding of DNA to CooA induces a further displacement of the C-helix in the same direction during transition to the complete active conformation. The Fe-CO and C-O stretching bands showed frequency shifts upon DNA binding, but the Fe-His stretching band did not. Moreover, CO-geminate recombination was more efficient in the DNA-bound state. These results suggest that the C-helix displacement in the DNA-bound form causes the CO binding pocket to narrow and become more negative.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism*
  • Carbon Monoxide / chemistry
  • DNA / chemistry*
  • Electrons
  • Heme / chemistry
  • Hemeproteins / chemistry*
  • Hemeproteins / metabolism*
  • Iron / metabolism
  • Kinetics
  • Ligands
  • Models, Molecular
  • Molecular Conformation
  • Protein Binding
  • Protein Conformation
  • Protein Structure, Secondary
  • Rhodospirillum rubrum / metabolism
  • Spectrophotometry, Ultraviolet / methods*
  • Spectrum Analysis, Raman
  • Time Factors
  • Trans-Activators / chemistry*
  • Trans-Activators / metabolism*
  • Tryptophan / chemistry
  • Ultraviolet Rays

Substances

  • Bacterial Proteins
  • CooA protein, Rhodospirillum rubrum
  • Hemeproteins
  • Ligands
  • Trans-Activators
  • Heme
  • Carbon Monoxide
  • Tryptophan
  • DNA
  • Iron