Phytochromes are photoreceptors that regulate many aspects of plant growth and development such as the time of flowering, seed germination, elongation of seedlings, leaves size, shape and number of leaves in response to red and far-red light signals. It exists two spectrally distinct red absorbing Pr and far-red absorbing Pfr forms. The photosensing module (PSM) of canonical plant phytochromes consists of a PAS-GAF-PHY domain. The PSM of Arabidopsis thaliana phytochrome B (AtphyB) now has a solved three-dimensional protein structure (PDB ID: 4OUR).
Based on the “toggle” model for photoconversion, molecular modeling studies for PMS of Avena sativa phytochrome A (AsphyA) and AtphyB were performed to obtain structural information of plant phytochrome. To predict high-quality model structures for the Pr and Pfr forms of phytochromes, homology modeling studies were performed using AtphyB, Syn-Cph1 (PDB ID: 2VEA), SyB-Cph1 (PDB ID: 2KLI), and DrBphP (PDB ID: 5C5K) as a template structure. Based on the experimental data that the PSM of phytochrome could have kinase activity, we performed a molecular docking calculation and molecular dynamics (MD) simulation to identify the ATP binding site and compared the wild-type (WT) and kinase mutants (K411L, T418D, and D422R). When mutated Tyr residue in GAF domain, the phytochrome shows light-independent characteristics. Thus, we performed MD simulation to compare the structural difference between WT and mutant (Y303V). Further comparison between WT and mutant forms were carried out on the basis of a number of hydrogen bonding, Cα distance, and calculation of distance between important atoms. Thus, these results showed that identification of the putative ATP-binding site in PHY domain and role of the Tyr residues in GAF domain. This structural information will be useful to understanding the mechanism of light signal transduction in plant phytochromes.