Protein Family Models

Date:

2024-08-14

The GAF domain is named after some of the proteins it is found in, including cGMP-specific phosphodiesterases, adenylyl cyclases and FhlA. It is also found in guanylyl cyclases and phytochromes [1,2]. The structure of a GAF domain shows that the domain shares a similar fold with the PAS domain [3]. This domain can bind O2, CO and NO (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [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;17:1551-1557. [3]. 11032796. Structure of the GAF domain, a ubiquitous signaling motif and a new class of cyclic GMP receptor. Ho YS, Burden LM, Hurley JH;. EMBO J. 2000;19:5288-5299. (from Pfam)

Date:

2024-10-16

This Pfam entry includes some of the AAA proteins not detected by the Pfam:PF00004 model. [1]. 7646486. A 200-amino acid ATPase module in search of a basic function. Confalonieri F, Duguet M;. Bioessays 1995;17:639-650. A large extension of the family. [2]. 9927482. AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Neuwald AF, Aravind L, Spouge JL, Koonin EV;. Genome Res 1999;9:27-43. (from Pfam)

Date:

2024-10-16

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

Date:

2024-08-14

AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2]. [1]. 7646486. A 200-amino acid ATPase module in search of a basic function. Confalonieri F, Duguet M;. Bioessays 1995;17:639-650. A large extension of the family. [2]. 9927482. AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Neuwald AF, Aravind L, Spouge JL, Koonin EV;. Genome Res 1999;9:27-43. (from Pfam)

Date:

2024-10-16

nitric oxide reductase transcription regulator similar to the Escherichia coli anaerobic nitric oxide reductase transcription regulator NorR, which is required for the expression of anaerobic nitric oxide reductase

Date:

2023-03-10

Required for the expression of anaerobic nitric oxide (NO) reductase; acts as a transcriptional activator for the norVW operon

Gene:

norR

Date:

2021-08-04