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 family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90. [1]. 18361456. Crystal structure of a novel non-Pfam protein AF1514 from Archeoglobus fulgidus DSM 4304 solved by S-SAD using a Cr X-ray source. Li Y, Bahti P, Shaw N, Song G, Chen S, Zhang X, Zhang M, Cheng C, Yin J, Zhu JY, Zhang H, Che D, Xu H, Abbas A, Wang BC, Liu ZJ;. Proteins 2008;71:2109-13. (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

Dimerisation and phospho-acceptor domain of histidine kinases. [1]. 9989504. Structure of CheA, a signal-transducing histidine kinase. Bilwes AM, Alex LA, Crane BR, Simon MI;. Cell 1999;96:131-141. [2]. 18361456. Crystal structure of a novel non-Pfam protein AF1514 from Archeoglobus fulgidus DSM 4304 solved by S-SAD using a Cr X-ray source. Li Y, Bahti P, Shaw N, Song G, Chen S, Zhang X, Zhang M, Cheng C, Yin J, Zhu JY, Zhang H, Che D, Xu H, Abbas A, Wang BC, Liu ZJ;. Proteins 2008;71:2109-13. (from Pfam)

Date:

2024-10-16

This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain. [1]. 7699720. Response regulators of bacterial signal transduction systems: selective domain shuffling during evolution. Pao GM, Saier MH;. J Mol Evol 1995;40:136-154. (from Pfam)

Date:

2024-10-16