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Links from Protein

Items: 18

1.

Sigma-54 interaction domain

GO Terms:
Molecular Function:
ATP binding (GO:0005524)
Biological Process:
regulation of DNA-templated transcription (GO:0006355)
Molecular Function:
transcription factor binding (GO:0008134)
Date:
2024-08-14
Family Accession:
NF025885.5
Method:
HMM
2.

helix-turn-helix domain-containing protein

GO Terms:
Molecular Function:
sequence-specific DNA binding (GO:0043565)
Date:
2024-08-14
Family Accession:
NF014950.5
Method:
HMM
3.

GAF domain-containing protein

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)

GO Terms:
Molecular Function:
protein binding (GO:0005515)
Date:
2024-10-16
Family Accession:
NF013736.5
Method:
HMM
4.

sigma 54-interacting transcriptional regulator

GO Terms:
Molecular Function:
ATP binding (GO:0005524)
Biological Process:
regulation of DNA-templated transcription (GO:0006355)
Molecular Function:
transcription factor binding (GO:0008134)
Date:
2024-08-14
Family Accession:
NF012385.5
Method:
HMM
5.

PAS domain-containing protein

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. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 9301332. PAS domain S-boxes in archaea, bacteria and sensors for oxygen and redox. Zhulin IB, Taylor BL, Dixon R;. Trends Biochem Sci 1997;22:331-333. [2]. 7756254. 1.4 A structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore. Borgstahl GE, Williams DR, Getzoff ED;. Biochemistry 1995;34:6278-6287. [3]. 9382818. PAS: a multifunctional domain family comes to light. Ponting CP, Aravind L;. Curr Biol 1997;7:674-677. [4]. 15009198. The PAS fold: a redefination of the PAS domain based upon structural prediction. Hefti MH, Francoijs KJ, de Vries SC, Dixon R, Vervoort J;. Eur J Biochem 2004;271:1198-1208. (from Pfam)

GO Terms:
Biological Process:
regulation of DNA-templated transcription (GO:0006355)
Date:
2024-10-16
Family Accession:
NF013179.5
Method:
HMM
6.
new record, indexing in progress
Family Accession:
7.
new record, indexing in progress
Family Accession:
8.
new record, indexing in progress
Family Accession:
9.
new record, indexing in progress
Family Accession:
10.
new record, indexing in progress
Family Accession:
11.
new record, indexing in progress
Family Accession:
12.
new record, indexing in progress
Family Accession:
13.
new record, indexing in progress
Family Accession:
14.
new record, indexing in progress
Family Accession:
15.

dihydroxyacetone kinase operon transcriptional regulator DhaR

Positively regulates the dhaKLM operon from a sigma-70 promoter

Gene:
dhaR
GO Terms:
Molecular Function:
ATP binding (GO:0005524)
Biological Process:
regulation of DNA-templated transcription (GO:0006355)
Molecular Function:
transcription factor binding (GO:0008134)
Molecular Function:
sequence-specific DNA binding (GO:0043565)
Date:
2022-03-31
Family Accession:
NF008485.2
Method:
HMM
16.
new record, indexing in progress
Family Accession:
17.
new record, indexing in progress
Family Accession:
18.

PTS-dependent dihydroxyacetone kinase operon transcriptional regulator DhaR

PTS-dependent dihydroxyacetone kinase operon transcriptional regulator DhaR positively regulates the dhaKLM operon from a sigma-70 promoter

Date:
2019-07-02
Family Accession:
11485334
Method:
Sparcle
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