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This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyse ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regul ...
This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyse ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalysed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54. This domain can bind biliverdine and phycocyanobilin (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Phytochromes are a family of biliprotein photoreceptors ubiquitous in plants but also present in many bacteria and fungi [1,2]. The protein undergoes reversible photochemical conversion between red light- and far-red light-absorbing states (Pr and Pf ...
Phytochromes are a family of biliprotein photoreceptors ubiquitous in plants but also present in many bacteria and fungi [1,2]. The protein undergoes reversible photochemical conversion between red light- and far-red light-absorbing states (Pr and Pfr, respectively). Phytochromes are usually homodimeric, each protomer containing a covalently-attached, linear tetrapyrrole chromophore that isomerizes in light, leading to state transition. Prokaryotic phytochromes signal enzymatically from a C-terminal histidine kinase module active in the Pr state, thereby regulating diverse biological aspects such as pigmentation and the developmental program. Conversely, plant phytochromes signal as Pfr through interactions with partner molecules that have extensive regulatory effects throughout the plant genome [2]. This domain is found in the central region of phytochrome proteins and structurally related to Pfam:PF01590 [1], which is generally located immediately N-terminal to this domain. Compared with Pfam:PF01590, this domain carries an additional tongue-like hairpin loop between the fifth beta-sheet and the sixth alpha-helix which functions to seal the chromophore pocket and stabilising the photoactivated far-red-absorbing state (Pfr) [1]. The tongue reaches back to contact the GAF domain, generally sealing the chromophore pocket and stabilising the Pfr state. The conformation of the tongue changes radically upon Pr-Pfr photoconversion, an effect that is probably central to signal regulation [3].
The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya.