Protein Family Models

This family of bacterial transcriptional regulators includes the glycerol operon regulatory protein and acetate operon repressor both of which are members of the iclR family. These proteins have a Helix-Turn-Helix motif at the N-terminus. However this family covers the C-terminal region that binds to regulatory substrates including Glyoxylate, allantoin/ate, indole, aromatic hydrocarbons, sugar acids, succinic semialdehyde, benzoate derivatives, ascorbic acid, glycerol-3-phosphate, glyceraldehyde-3-phosphate and pyruvate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 1995429. Primary structure of the intergenic region between aceK and iclR in the Escherichia coli chromosome. Galinier A, Bleicher F, Negre D, Perriere G, Duclos B, Cozzone AJ, Cortay JC;. Gene 1991;97:149-150. [2]. 3225846. Structure and regulation of controlling sequences for the Streptomyces coelicolor glycerol operon. Smith CP, Chater KF;. J Mol Biol 1988;204:569-580. (from Pfam)

Date:

2024-10-16

Date:

2024-08-14

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). Discovery and naming of the GAF domain. [1]. 9433123. The GAF domain: an evolutionary link between diverse phototransducing proteins. Aravind L, Ponting CP;. Trends Biochem Sci 1997;22:458-459. [2]. 20004158. Cyclic nucleotide binding GAF domains from phosphodiesterases: structural and mechanistic insights. Heikaus CC, Pandit J, Klevit RE;. Structure. 2009;17:. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-10-16