Nature 438, 325-331 (17 November 2005) | doi:10.1038/nature04118; Received 27 May 2005; Accepted 9 August 2005

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

Jeremiah R. Wagner1, Joseph S. Brunzelle3, Katrina T. Forest2 & Richard D. Vierstra1

  1. Department of Genetics,
  2. Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706 USA
  3. Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois 60439, USA

Correspondence to: Katrina T. Forest2 Correspondence and requests for materials should be addressed to K.T.F. (Email: Atomic coordinates and structure factor amplitudes have been deposited in the Protein Data Bank (accession code 1ZTU).


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 Å 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.


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