Domain structures of phytochromes. (a) The modular nature of phytochromes. Phytochromes consist of two functionally separable regions: an amino-terminal photosensing domain and a carboxy-terminal domain that is involved in dimerization of phytochrome polypeptide chains and in generating the output signal. (b) Conserved phytochrome domains: NTE, plant-specific amino-terminal extension; PLD, PAS-like domain; GAF, a domain distantly related to PAS and found in phytochromes and cGMP-specific phosphodiesterases; PHY, a domain distantly related to PAS and specific to phytochromes; HKD, histidine kinase domain containing a phosphoacceptor His residue and motifs characteristic of functional histidine kinases; HKRD, histidine kinase related domain lacking a phosphoacceptor His residue and motifs characteristic of histidine kinases; HisKA, histidine kinase A domain-related; HisK-ATPase, histidine kinase ATPase superfamily domain. The response regulator (RR)-like domain shown bracketed in Cph and Bph is found in a minority of these proteins but is common in Fph proteins. (c) The non-photoreversible chromophore-binding fragment of Bph that was used for determination of the three-dimensional structures published in [25, 29, 30]. Its structure determines the absorption spectrum of the Pr form. For comparison, the photoreversible fragment containing the PHY domain is also diagrammed. Its structure will provide information about the nature of the conformational change between Pr and Pfr.