Residues Clustered in the Light-Sensing Knot of Phytochrome B are Necessary for Conformer-Specific Binding to Signaling Partner PIF3
The Arabidopsis phyB sequence was threaded onto the Deinococcus phytochrome. A) Superimposition of ribbon diagrams of the homology model of Arabidopsis phyB N terminus and experimentally determined structure of Deinococcus phy (pdb: 1ztu). Deinococcus is represented in blue and Arabidopsis in green. There is complete agreement between the main chain positions of the model and the experimental structure in the chromophore binding region. The cys24 residue of Deinococcus phytochrome is indicated in magenta. The chromophore binding cys357 of Arabidopsis phyB is indicated in purple, with the sulfur atom highlighted, showing the conserved spatial location of the chromophore binding cysteine. B) Space filling diagram of the predicted phyB structure, with three of the Class II amino acid residues identified in this study shown in yellow (G348) or red (R110, G111), showing that they are at least partially exposed to the surface, and located in close proximity to one another in the cleft at the junction of the PAS and GAF subdomains. C) Ribbon diagram of the predicted phyB structure with the three apparently solvent exposed residues shown in red or yellow space filling format and the chromophore attachment site shown in green space filling format. The distance between G348 and the chromophore attachment site (C357) is indicated by the dashed line.