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

Nature volume 438, pages 325–331 (2005)Cite this article

Abstract

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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Figure 1: Three-dimensional structure of Dr CBD.
Figure 2: Structure of the deep trefoil knot.
Figure 3: Structure and linkage of biliverdin within Dr CBD.
Figure 4: Structural conservation and evolution of phytochrome photoreceptors.

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Acknowledgements

We thank B. Karniol, S. Beale and K. Satyshur for technical advice and acknowledge the Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor for the support of this research program. Use of the Advanced Photon Source was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences. This work was supported by grants from the US National Science Foundation (R.D.V. and K.T.F.), the US Department of Energy (R.D.V.), and the W.M. Keck Foundation (K.T.F.). Author Contributions J.R.W. purified protein and grew and characterized crystals; J.S.B. collected data and carried out initial phase determination; K.T.F. and J.R.W. phased, modelled, refined and validated structure; R.D.V. initiated collaboration; K.T.F. designed structure experiments; J.R.W., K.T.F. and R.D.V. interpreted the structure and prepared the manuscript and figures.

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Authors and Affiliations

  1. Department of Genetics,

    Jeremiah R. Wagner & Richard D. Vierstra

  2. Department of Bacteriology, University of Wisconsin-Madison, Wisconsin, 53706, Madison, USA

    Katrina T. Forest

  3. Life Sciences Collaborative Access Team, Northwestern University, Illinois, 60439, Argonne, USA

    Joseph S. Brunzelle

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Correspondence to Katrina T. Forest.

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Atomic coordinates and structure factor amplitudes have been deposited in the Protein Data Bank (accession code 1ZTU). Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

Supplementary information

Supplementary Table 1

This table includes all data collection and scaling statistics as well as refinement statistics for the crystal structure determination of phytochrome. (DOC 48 kb)

Supplementary Figure 1

Spectra of native, selenomethionine labeled, and crystalline DrCBD. (PDF 266 kb)

Supplementary Figure 2

Sequence alignment of plant, cyanobacterial and bacterial phytochromes with secondary structure elements indicated (PDF 300 kb)

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Wagner, J., Brunzelle, J., Forest, K. et al. A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome. Nature 438, 325–331 (2005). https://doi.org/10.1038/nature04118

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