Structure of the Biliverdin Cofactor in the Pfr State of Bathy and Prototypical Phytochromes

• Published in: The Journal of biological chemistry 2013-06, Vol.288 (23), p.16800-16814
• Main Authors: Salewski, Johannes, Escobar, Francisco Velazquez, Kaminski, Steve, von Stetten, David, Keidel, Anke, Rippers, Yvonne, Michael, Norbert, Scheerer, Patrick, Piwowarski, Patrick, Bartl, Franz, Frankenberg-Dinkel, Nicole, Ringsdorf, Simone, Gärtner, Wolfgang, Lamparter, Tilman, Mroginski, Maria Andrea, Hildebrandt, Peter
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - chemistry; Binding Sites; Computer Modeling; Infrared Spectroscopy; Molecular Biophysics; Photoreceptors; Phytochrome; Phytochrome - chemistry; Pseudomonas aeruginosa - chemistry; QM/MM Calculations; Raman Spectroscopy; Resonance Raman; Spectroscopy
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M113.457531

Phytochromes act as photoswitches between the red- and far-red absorbing parent states of phytochromes (Pr and Pfr). Plant phytochromes display an additional thermal conversion route from the physiologically active Pfr to Pr. The same reaction pattern is found in prototypical biliverdin-binding bacteriophytochromes in contrast to the reverse thermal transformation in bathy bacteriophytochromes. However, the molecular origin of the different thermal stabilities of the Pfr states in prototypical and bathy bacteriophytochromes is not known. We analyzed the structures of the chromophore binding pockets in the Pfr states of various bathy and prototypical biliverdin-binding phytochromes using a combined spectroscopic-theoretical approach. For the Pfr state of the bathy phytochrome from Pseudomonas aeruginosa, the very good agreement between calculated and experimental Raman spectra of the biliverdin cofactor is in line with important conclusions of previous crystallographic analyses, particularly the ZZEssa configuration of the chromophore and its mode of covalent attachment to the protein. The highly homogeneous chromophore conformation seems to be a unique property of the Pfr states of bathy phytochromes. This is in sharp contrast to the Pfr states of prototypical phytochromes that display conformational equilibria between two sub-states exhibiting small structural differences at the terminal methine bridges A-B and C-D. These differences may mainly root in the interactions of the cofactor with the highly conserved Asp-194 that occur via its carboxylate function in bathy phytochromes. The weaker interactions via the carbonyl function in prototypical phytochromes may lead to a higher structural flexibility of the chromophore pocket opening a reaction channel for the thermal (ZZE → ZZZ) Pfr to Pr back-conversion. Background: The Pr and Pfr parent states of prototypical and bathy bacteriophytochromes exhibit different thermal stabilities. Results: Unlike bathy phytochromes, the biliverdin cofactor of prototypical phytochromes displays distinct conformational heterogeneity in Pfr. Conclusion: This heterogeneity enables thermal Pfr to Pr conversion in prototypical phytochromes. Significance: Understanding thermal deactivation of the signaling Pfr state is essential for elucidating the molecular function of phytochromes.