A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome

Nature. 2005 Nov 17;438(7066):325-31. doi: 10.1038/nature04118.


Phytochromes are red/far-red light photoreceptors that direct photosensory responses across the bacterial, fungal and plant kingdoms. These include photosynthetic potential and pigmentation in bacteria as well as chloroplast development and photomorphogenesis in plants. Phytochromes consist of an amino-terminal region that covalently binds a single bilin chromophore, followed by a carboxy-terminal dimerization domain that often transmits the light signal through a histidine kinase relay. Here we describe the three-dimensional structure of the chromophore-binding domain of Deinococcus radiodurans phytochrome assembled with its chromophore biliverdin in the Pr ground state. Our model, refined to 2.5 A resolution, reaffirms Cys 24 as the chromophore attachment site, locates key amino acids that form a solvent-shielded bilin-binding pocket, and reveals an unusually formed deep trefoil knot that stabilizes this region. The structure provides the first three-dimensional glimpse into the photochromic behaviour of these photoreceptors and helps to explain the evolution of higher plant phytochromes from prokaryotic precursors.

Publication types

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

MeSH terms

  • Bile Pigments / metabolism
  • Biliverdine / metabolism
  • Binding Sites
  • Crystallization
  • Deinococcus / chemistry*
  • Evolution, Molecular
  • Histidine Kinase
  • Light Signal Transduction / radiation effects*
  • Light*
  • Models, Molecular
  • Phytochrome / chemistry*
  • Phytochrome / metabolism*
  • Phytochrome / radiation effects
  • Protein Folding
  • Protein Kinases / metabolism
  • Protein Structure, Tertiary


  • Bile Pigments
  • Phytochrome
  • Protein Kinases
  • Histidine Kinase
  • Biliverdine

Associated data

  • PDB/1ZTU