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Coordination of the Biliverdin D-ring in Bacteriophytochromes


Phytochrome proteins translate light into biochemical signals in plants, fungi and microorganisms. Light cues are absorbed by a bilin chromophore, leading to an isomerization and a rotation of the D-ring. This relays the signal to the protein matrix. A set of amino acids, which is conserved across the phytochrome superfamily, holds the chromophore in the binding pocket. However, the functional role of many of these amino acids is not yet understood. Here, we investigate the hydrogen bonding network which surrounds the D-ring of the chromophore in the resting Pr state. We use UV/VIS spectroscopy, infrared absorption spectroscopy and X-ray crystallography to compare the photosensory domains from Deinococcus radiodurans the phytochrome 1 from Stigmatella aurantiaca and a D.radiodurans H290T mutant. In the latter two, an otherwise conserved histidine next to the D-ring is replaced by a threonine. Our infrared absorption data indicate that the carbonyl of the D-ring is more strongly coordinated by hydrogen bonds when the histidine is missing. This is in apparent contrast with the crystal structure of the PAS-GAF domain of phytochrome 1 from Stigmatella aurantiaca (pdb code 4RPW), which did not resolve any obvious binding partners for the D-ring carbonyl. We present a new crystal structure of the H290T mutant of the PAS-GAF from Deinococcus radiodurans . The structure reveals at a resolution of 1.4 Å density for additional water molecules, which fill the void created by the mutation. Two of the waters are significantly disordered, suggesting that flexibility might be important for the photoconversion. Finally, we report spectra that explain why the histidine-less phytochromes do not reach high levels of Pfr in the photoequilibrium. The study highlights the importance of water molecules and the hydrogen bonding network around the chromophore in controlling the isomerization reaction in phytochromes.

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Publication details

The article was received on 15 Mar 2018, accepted on 13 Jun 2018 and first published on 14 Jun 2018

Article type: Paper
DOI: 10.1039/C8CP01696H
Citation: Phys. Chem. Chem. Phys., 2018, Accepted Manuscript
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    Coordination of the Biliverdin D-ring in Bacteriophytochromes

    N. Lenngren, P. Edlund, H. Takala, B. Stucki-Buchli, J. Rumfeldt, I. Peshev, H. Häkkänen, S. Westenhoff and J. Ihalainen, Phys. Chem. Chem. Phys., 2018, Accepted Manuscript , DOI: 10.1039/C8CP01696H

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