|
|
ssDNA-binding transcriptional regulator domain superfamily
SCOP classification
InterPro annotation
| Cross references | IPR009044 SSF54447 Protein matches |
| Abstract | This entry represents a ssDNA-binding transcriptional regulator domain consisting of a helix-swapped dimer of beta(4)-alpha motifs. This domain is found as a C-terminal domain in the transciptional co-activator PC4 (where it is a dimer of two separate motifs), and in the plant transciprional regulator PBF-2 (where it is a single chain domain formed by a tandem repeat of two motifs).
Transcriptional regulators play a critical role in controlling the level of transcription from specific genes in response to different stimuli. Members of this family of transcriptional regulators, which preferentially bind single-stranded DNA, include PBF-2 from plants, the mammalian nuclear factor 1-X (NF1-X), and positive cofactor 4 (PC4). These proteins are structurally similar, consisting of a helix-swapped dimer of beta(4)-alpha motifs.
The plant defence transcription factor PBF-2 is comprised of four p24 subunits that interact through a helix-loop-helix motif to produce a central pore [ 12080340]. PBF-2 functions as part of the plant¿s defence system in response to the detection of a pathogen. Upon stimulation, PBF-2 induces several signal transduction pathways leading to changes in the expression of defence genes, including the pathogenesis-related (PR) genes.
NF1-X is one of several NF1 proteins that function as transcription factors. NF1-X consists of two functionally distinct domains: a conserved N-terminal DNA-binding domain and a C-terminal transcriptional regulatory domain. NF1-X binds to the promoter for the 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase gene [10432316].
PC4 (or P15) possess the ability to co-activate and suppress transcription via its DNA-binding activity. PC4 has been shown to stimulate transcription in vitro with diverse activators, including VP16, thyroid hormone receptor, BRCA-1, often involving TFIIA. PC4 and TFIIA are thought to facilitate the assembly of the pre-initiation complex. The repressive activity of PC4 can be alleviated by the transcription factor TFIIH, which protects promoters from PC4 repression [12590132]. PC4 consists of two domains: an N-terminal regulatory domain and a C-terminal cryptic DNA-binding domain. The protein acts as a dimer with two ssDNA binding channels running in opposite directions to each other [9360603]. |
InterPro database
Functional annotation
| General category | Regulation |
| Detailed category | DNA-binding |
Function annotation of SCOP domain superfamilies
Jump to [ Top of page · SCOP classification · InterPro annotation · Functional annotation ]
Internal database links
The SUPERFAMILY hidden Markov model library has been used to carry
out SCOP domain assignments to all genomes at the superfamily level. Click on the 'Genome Assignments'
icon above to view the genome assignments for this superfamily.
Alignments of sequences to Alignments of sequences to 6 models
in this superfamily are available by clicking on the superfamily level 'Alignments' icon above. PDB sequences less than 40% identical
are shown by default, but any other sequences may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own.
It is possible to browse and view the proteins in the genomes which have
different combinations of domains including a ssDNA-binding transcriptional regulator domain domain. Click on the 'Domain Combinations' icon.
To view the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom click on the 'TaxViz' icon above. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.
Undirected domain occurrence networks are available for all superfamilies. Nodes in these networks represent genomes. Connections between nodes represent the presence of domain architectures, which contain the superfamily of interest, in both genomes.
There are 6 hidden Markov models representing the ssDNA-binding transcriptional regulator domain superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be viewed by clicking on the icon above.
Jump to [ Top of page · SCOP classification · InterPro annotation · Functional annotation · Internal database links ]
|
0
