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:

2024-08-14

Date:

2024-08-14

This entry represents a TIM barrel domain found at the C terminus of a number of PEP (phosphoenolpyruvate)-utilising proteins. In PPDK (Pyruvate phosphate dikinase) this C-terminal domain has been shown to be a PEP-binding domain [1]. [1]. 18052212. Swiveling domain mechanism in pyruvate phosphate dikinase.. Lim K, Read RJ, Chen CC, Tempczyk A, Wei M, Ye D, Wu C,. Dunaway-Mariano D, Herzberg O;. Biochemistry. 2007;46:14845-14853. (from Pfam)

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. 200. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-08-14

This domain is a "swivelling" beta/beta/alpha domain which is thought to be mobile in all proteins known to contain it. [1]. 8610096. Swiveling-domain mechanism for enzymatic phosphotransfer between. remote reaction sites.. Herzberg O, Chen CC, Kapadia G, McGuire M, Carroll LJ, Noh SJ,. Dunaway-Mariano D;. Proc Natl Acad Sci U S A 1996;93:2652-2657. (from Pfam)

Date:

2024-08-14

This HMM recognizes a distinct clade of phophoenolpyruvate (PEP)-dependent enzymes. Most members are known or deduced to function as the phosphoenolpyruvate-protein phosphotransferase (or enzyme I) of PTS sugar transport systems. However, some species with both a member of this family and a homolog of the phosphocarrier protein HPr lack a IIC component able to serve as a permease. An HPr homolog designated NPr has been implicated in the regulation of nitrogen assimilation, which demonstrates that not all phosphotransferase system components are associated directly with PTS transport.

Gene:

ptsP

Date:

2024-06-14

phosphoenolpyruvate--protein phosphotransferase transfers the phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein

Date:

2017-02-17