Conclusion
Assessment
Binding Mode
Motif Status
Notes
Comments
Known motif
1 Monomer or homomultimer
100 perc ID - in vitro
Binds DNA in the pre-initiation complex
Description
Description:
TATA-box binding protein [Source:HGNC Symbol;Acc:HGNC:11588]
Entrez Summary
TBA
Ensembl ID:
ENSG00000112592
External Link:
T150542_1.02
Interpro
IPR000814 ; IPR030491 ;
Protein Domain:
Protein: ENSP00000230354DBD: TBPOther: DDHD, DUF4746, EPL1, MMR1, PresenilinProtein: ENSP00000375942DBD: TBPOther: DDHD, DUF4746, EPL1, MMR1, PresenilinProtein: ENSP00000400008DBD: TBPOther: DDHD, DUF4746, EPL1, MMR1, Presenilin, SpoIIP, TFIProtein: ENSP00000442132DBD: TBPOther: DDHD, EPL1, MMR1, PresenilinProtein: ENSP00000416482DBD: TBPOther: DUF4746, SpoIIP, TFIIA
Previous Annotations
Source
Annotation
TF-CAT classification
No PMIDS:
Vaquerizas 2009 TF classification
"a " Has direct evidence of TF function;
"b " Has evidence for an orthologous TF;
"c " contains likely DBDs, but has no functional evidence;
"x " is an unlikely TF such as predicted gene, genes with likely non-specific DBDs or that have function outside transcription;
"other " category contains proteins without clear DBDs they curated from external sources.
No
CisBP considers it as a TF?
Yes
TFclass considers it as a TF?
Yes
Has GO:0003700 "transcription factor activity, sequence-specific DNA binding"
No
GO-Info
GO:0001034 sequence-specific DNA binding RNA polymerase III transcription factor activity IMP - PMID:26638071
Initial Assessment
1a1 Protein has a high confidence PWM (HT-SELEX, PBM or B1H model) or there is a crystal structure that supports sequence specific DNA binding;
1a2 There is high confidence data for a close ortholog (as defined in CisBP);
2a1 There is lower confidence direct evidence, such as a Jaspar, Hocomoco or Transfac model;
2a2 There is lower confidence evidence for an close ortholog;
3a There is decent circumstantial evidence for its role as a TF or not;
4a Two or more datasets predict it as a TF;
5a One of the source datasets predicts is as a TF
1a1, Direct HQ evidence
TF has conditional DNA-binding requirements
DNA-Binding
Published Motif Data
Structure
Experimental History
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The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step [1]. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription.", "database": "PfamA", "aliStart": 47, "scoreName": "E-value", "accession": "PF03153.11", "start": 14, "score": 0.0078, "identifier": "Transcription factor IIA, alpha/beta subunit", "type": "DBD", "aliEnd": 125}}], "length": 208}
{"regions": [{"startStyle": "curved", "end": 224, "endStyle": "curved", "aliStart": 144, "text": "TBP", "colour": "#228B22", "aliEnd": 223, "start": 142, "href": "http://pfam.xfam.org/family/PF00352.19", "type": "pfama", "display": "true", "metadata": {"end": 224, "description": "The TATA-binding protein (TBP) is a general transcription factor that binds specifically to a DNA sequence called the TATA box. ", "database": "PfamA", "aliStart": 144, "scoreName": "E-value", "accession": "PF00352.19", "start": 142, "score": 3.5999999999999996e-66, "identifier": "Transcription factor TFIID (or TATA-binding protein, TBP)", "type": "DBD", "aliEnd": 223}}, {"startStyle": "curved", "end": 315, "endStyle": "curved", "aliStart": 232, "text": "TBP", "colour": "#228B22", "aliEnd": 313, "start": 232, "href": "http://pfam.xfam.org/family/PF00352.19", "type": "pfama", "display": "true", "metadata": {"end": 315, "description": "The TATA-binding protein (TBP) is a general transcription factor that binds specifically to a DNA sequence called the TATA box. ", "database": "PfamA", "aliStart": 232, "scoreName": "E-value", "accession": "PF00352.19", "start": 232, "score": 3.5999999999999996e-66, "identifier": "Transcription factor TFIID (or TATA-binding protein, TBP)", "type": "DBD", "aliEnd": 313}}, {"startStyle": "straight", "end": 212, "endStyle": "jagged", "aliStart": 22, "text": "EPL1", "colour": "#9999ff", "aliEnd": 103, "start": 20, "href": "http://pfam.xfam.org/family/PF10513.7", "type": "pfama", "display": "true", "metadata": {"end": 212, "description": "This is a family of EPL1 (Enhancer of polycomb-like) proteins. The EPL1 protein is a member of a histone acetyltransferase complex which is involved in transcriptional activation of selected genes [3].", "database": "PfamA", "aliStart": 22, "scoreName": "E-value", "accession": "PF10513.7", "start": 20, "score": 2.2e-05, "identifier": "Enhancer of polycomb-like", "type": "DBD", "aliEnd": 103}}, {"startStyle": "jagged", "end": 236, "endStyle": "jagged", "aliStart": 32, "text": "DDHD", "colour": "#9999ff", "aliEnd": 88, "start": 13, "href": "http://pfam.xfam.org/family/PF02862.15", "type": "pfama", "display": "true", "metadata": {"end": 236, "description": "The DDHD domain is 180 residues long and contains four conserved residues that may form a metal binding site. The domain is named after these four residues. This pattern of conservation of metal binding residues is often seen in phosphoesterase domains. This domain is found in retinal degeneration B proteins, as well as a family of probable phospholipases. It has been shown that this domain is found in a longer C terminal region that binds to PYK2 tyrosine kinase. These proteins have been called N-terminal domain-interacting receptor (Nir1, Nir2 and Nir3) [1]. This suggests that this region is involved in functionally important interactions in other members of this family.", "database": "PfamA", "aliStart": 32, "scoreName": "E-value", "accession": "PF02862.15", "start": 13, "score": 0.00022999999999999998, "identifier": "DDHD domain", "type": "DBD", "aliEnd": 88}}, {"startStyle": "jagged", "end": 155, "endStyle": "jagged", "aliStart": 34, "text": "Presenilin", "colour": "#9999ff", "aliEnd": 92, "start": 7, "href": "http://pfam.xfam.org/family/PF01080.15", "type": "pfama", "display": "true", "metadata": {"end": 155, "description": "Mutations in presenilin-1 are a major cause of early onset Alzheimer's disease [2]. It has been found that presenilin-1 (Swiss:P49768) binds to beta-catenin in-vivo [4]. This family also contains SPE proteins from C.elegans.", "database": "PfamA", "aliStart": 34, "scoreName": "E-value", "accession": "PF01080.15", "start": 7, "score": 0.00081, "identifier": "Presenilin", "type": "DBD", "aliEnd": 92}}, {"startStyle": "jagged", "end": 180, "endStyle": "jagged", "aliStart": 33, "text": "MMR1", "colour": "#9999ff", "aliEnd": 87, "start": 5, "href": "http://pfam.xfam.org/family/PF08505.8", "type": "pfama", "display": "true", "metadata": {"end": 180, "description": "Myo2p, a class V myosin, is essential for mitochondrial distribution, class V being vital for organelle distribution in S. cerevisiae. It is the myosin essential for mitochondrial distribution. The established mechanism for distribution of cellular components by class V myosins is that they interact with the cargo at the C-terminal tail domain and transport it along the actin cytoskeleton using the N-terminal motor domain. Cargo-specific myosin receptors act as the link between the myosin tail and cargo. Myo2 binds with MMR1 (mitochondrial Myo2p receptor-related 1), the receptor on cargo, via the C-terminal domain.", "database": "PfamA", "aliStart": 33, "scoreName": "E-value", "accession": "PF08505.8", "start": 5, "score": 0.0034, "identifier": "Mitochondrial Myo2 receptor-related protein", "type": "DBD", "aliEnd": 87}}], "length": 320}
{"regions": [{"startStyle": "jagged", "end": 137, "endStyle": "jagged", "aliStart": 53, "text": "DUF4746", "colour": "#9999ff", "aliEnd": 100, "start": 2, "href": "http://pfam.xfam.org/family/PF15928.3", "type": "pfama", "display": "true", "metadata": {"end": 137, "description": "This presumed domain is functionally uncharacterised. This domain is found in eukaryotes, and is typically between 247 and 324 amino acids in length. The family is found in association with Pfam:PF00085.", "database": "PfamA", "aliStart": 53, "scoreName": "E-value", "accession": "PF15928.3", "start": 2, "score": 0.0016, "identifier": "Domain of unknown function (DUF4746)", "type": "DBD", "aliEnd": 100}}, {"startStyle": "straight", "end": 127, "endStyle": "jagged", "aliStart": 53, "text": "SpoIIP", "colour": "#9999ff", "aliEnd": 98, "start": 17, "href": "http://pfam.xfam.org/family/PF07454.9", "type": "pfama", "display": "true", "metadata": {"end": 127, "description": "This family contains the bacterial stage II sporulation protein P (SpoIIP) (approximately 350 residues long). It has been shown that a block in polar cytokinesis in Bacillus subtilis is mediated partly by transcription of spoIID, spoIIM and spoIIP. This inhibition of polar division is involved in the locking in of asymmetry after the formation of a polar septum during sporulation [1]. Engulfment in Bacillus subtilis is mediated by two complementary systems: the first includes the proteins SpoIID, SpoIIM and SpoIIP (DMP) which carry out the engulfment, and the second includes the SpoIIQ-SpoIIIAGH (Q-AH) zipper, that recruits other proteins to the septum in a second-phase of the engulfment. The course of events follows as the incorporation firstly of SpoIIB into the septum during division to serve directly or indirectly as a landmark for localising SpoIIM and then SpoIIP and SpoIID to the septum. SpoIIP and SpoIID interact together to form part of the DMP complex [3]. SpoIIP itself has been identified as an autolysin with peptidoglycan hydrolase activity [2].", "database": "PfamA", "aliStart": 53, "scoreName": "E-value", "accession": "PF07454.9", "start": 17, "score": 0.0056, "identifier": "Stage II sporulation protein P (SpoIIP)", "type": "DBD", "aliEnd": 98}}, {"startStyle": "jagged", "end": 133, "endStyle": "jagged", "aliStart": 47, "text": "TFIIA", "colour": "#9999ff", "aliEnd": 125, "start": 11, "href": "http://pfam.xfam.org/family/PF03153.11", "type": "pfama", "display": "true", "metadata": {"end": 133, "description": "Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in Pfam:PF02268 and Pfam:PF02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step [1]. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription.", "database": "PfamA", "aliStart": 47, "scoreName": "E-value", "accession": "PF03153.11", "start": 11, "score": 0.0077, "identifier": "Transcription factor IIA, alpha/beta subunit", "type": "DBD", "aliEnd": 125}}], "length": 151}