PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons

Related Theme


PSI-SGKB [doi:10.3942/psi_sgkb/fm_2010_4]
Featured System - April 2010
Short description: Most animals, including ourselves, use sophisticated eyes to see light.

Most animals, including ourselves, use sophisticated eyes to see light. The light-sensing mechanism in these eyes uses a specialized molecule that absorbs light and changes shape. You might be surprised to hear that plants also see light, and they use a similar chemical trick to see it. They build phytochrome proteins that enfold a light-sensing chromophore, which also changes shape when it absorbs a photon of light. These phytochromes, along with several other types of light-sensing proteins, are essential for the life of the plant. They allow plants to sense the levels and location of light, and thus maximize their ability to absorb the light for photosynthesis.

Light and Shade

Phytochromes are particularly adept at sensing the difference between full sunlight and shade. Phytochromes adopt two different states, termed Pr and Pfr. The Pr state is best at absorbing red light, which is found in full-sun conditions. When it absorbs red light, phytochrome converts to the Pfr state, which is better at absorbing far-red light. Far-red light is more indicative of shade, which is typically depleted of red light. The Pfr state can then convert back to the Pr state either by absorbing far-red light, or if it is in the dark for a while, by slow thermal conversion. Thus, this switch between Pr and Pfr states allows the plant to see if it is in the sun or the shade.

Taking Action

Of course, the plant needs to make use of this information once it gets it. Switching of phytochrome to the Pfr state launches a host of changes in the plant, causing it, for instance, to bend or grow towards the light. Phytochrome is normally found in the cytoplasm of the plant cell, but when it converts to the Pfr state, it moves to the nucleus and modulates the expression of many genes responsible for growth and shape of the plant.

Light-sensing Machinery

Researchers at the CESG have revealed the atomic basis of the light-sensing machinery in phytochromes. They have recently solved the structure of an unusually small phytochrome in both the Pr and Pfr states. The small size of the phytochrome was important in this study: it allowed the researchers to solve the structure quickly using NMR spectroscopy. The structure of the Pr state was solved first (PDB entries 2k2n and 2koi), then the protein was irradiated with red light during the NMR experiment. This produced a mixture of half Pr and half Pfr, which was used to solve the structure of the Pfr state (PDB entry 2kli, shown here). The structures show that the motion of the chromophore is completely different than what was expected. To explore the structure and motion of the chromophore, click on the image below for an interactive Jmol.

The JSmol tab below displays an interactive JSmol

RBBP9 (PDB entries 2qs9)

Retinoblastoma binding protein 9 is a small enzyme with a typical serine protease catalytic site. The three catalytic residues (serine 75, histidine 165 and aspartate 138) are shown with white carbon atoms here. Use the buttons below to switch to a spacefilling representation to see the active site groove that presumably recognizes the target protein. The LxCxE loop, which is important for binding to retinoblastoma protein, is shown with green carbon atoms. Mutation of the leucine (the sidechain


  1. Ulijasz, A. T., Cornilescu, G., Cornilescu, C. C., Zhang, J., Rivera, M., Markley, J. L. and Vierstra, R. D. (2008) Structural basis for the photoconversion of a phytochrome to the activated Pfr form. Nature 463, 250-254.

  2. Cornilescu, G., Ulijasz, A. T., Cornilescu, C. C., Markley, J. L. and Vierstra, R. D. (2008) Solution structure of a cyanobacterial phytochrome GAF domain in the red-light-absorbing ground state. J. Mol. Biol. 383, 403-413.

  3. Rockwell, N. C. and Lagarias, J. C. (2006) The structure of phytochrome: a picture is worth a thousand spectra. The Plant Cell 18, 4-14.

  4. Wagner, J. R., Brunselle, J. S., Forest, K. T. and Vierstra, R. D. (2005) A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome. Nature 438, 325-331.

  5. Quail, P. H. (2002) Phytochrome photosensory signaling networks. Nat. Rev. Mol. Cell Biol. 3, 85-93.

Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health