RGD Reference Report - Structural bioinformatics of the general transcription factor TFIID. - Rat Genome Database

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Structural bioinformatics of the general transcription factor TFIID.

Authors: Malkowska, M  Kokoszynska, K  Rychlewski, L  Wyrwicz, L 
Citation: Malkowska M, etal., Biochimie. 2013 Apr;95(4):680-91. doi: 10.1016/j.biochi.2012.10.024. Epub 2012 Nov 9.
RGD ID: 9681723
Pubmed: PMID:23146842   (View Abstract at PubMed)
DOI: DOI:10.1016/j.biochi.2012.10.024   (Journal Full-text)

The Transcription Factor IID is a large macromolecular complex composed of the TATA-box binding protein (TBP) and a group of 13-14 conserved TBP-associated factors (TAFs). TAFs are known to regulate transcription at various levels - mediating transcription via interaction with activators, histone modifications; recognition and binding to promoters; acting as a platform for other Transcription Factors and RNA polymerase II. Despite numerous previous studies of the TFIID complex, the knowledge concerning the structure of its components, and thus the exact mechanism of its function, remains undetermined. To carry out an in-depth analysis of TFIID we performed the structural bioinformatic analysis of the TFIID complex. The sequence identity and similarity of 13.74% and 37.56%, respectively (calculated with PAM250 matrix) between M1 aminopeptidase protein and TAF2 and the high similarity of their putative secondary structures allowed us to model a large part of the TAF2 structure. The sequence analysis enabled the mapping of previously not fully characterized structural domains in well-studied TAF proteins (including the full histone domains of TAF4 and 12 or TAF3 and 8). In this study we provided detailed structural models for all the elements of human analyzed in the context of TFIID activity, along with indications of structural alterations within TFIID in various animal model species.



Molecular Pathway Annotations    Click to see Annotation Detail View

RGD Manual Annotations


  
Object SymbolSpeciesTermQualifierEvidenceWithNotesSourceOriginal Reference(s)
TAF1HumanRNA polymerase II transcription initiation pathway  TAS  RGD 
TAF10HumanRNA polymerase II transcription initiation pathway  TAS  RGD 
TAF11HumanRNA polymerase II transcription initiation pathway  TAS  RGD 
TAF12HumanRNA polymerase II transcription initiation pathway  TAS  RGD 
TAF13HumanRNA polymerase II transcription initiation pathway  TAS  RGD 
TAF15HumanRNA polymerase II transcription initiation pathway  TAS  RGD 
TAF2HumanRNA polymerase II transcription initiation pathway  TAS  RGD 
TAF3HumanRNA polymerase II transcription initiation pathway  TAS  RGD 
TAF4HumanRNA polymerase II transcription initiation pathway  TAS  RGD 
TAF5HumanRNA polymerase II transcription initiation pathway  TAS  RGD 
TAF6HumanRNA polymerase II transcription initiation pathway  TAS  RGD 
TAF7HumanRNA polymerase II transcription initiation pathway  TAS  RGD 
TAF8HumanRNA polymerase II transcription initiation pathway  TAS  RGD 
TAF9HumanRNA polymerase II transcription initiation pathway  TAS  RGD 
TBPHumanRNA polymerase II transcription initiation pathway  TAS  RGD 
Taf1MouseRNA polymerase II transcription initiation pathway  ISOTAF1 (Homo sapiens) RGD 
Taf1RatRNA polymerase II transcription initiation pathway  ISOTAF1 (Homo sapiens) RGD 
Taf10RatRNA polymerase II transcription initiation pathway  ISOTAF10 (Homo sapiens) RGD 
Taf10MouseRNA polymerase II transcription initiation pathway  ISOTAF10 (Homo sapiens) RGD 
Taf11RatRNA polymerase II transcription initiation pathway  ISOTAF11 (Homo sapiens) RGD 
Taf11MouseRNA polymerase II transcription initiation pathway  ISOTAF11 (Homo sapiens) RGD 
Taf12RatRNA polymerase II transcription initiation pathway  ISOTAF12 (Homo sapiens) RGD 
Taf12MouseRNA polymerase II transcription initiation pathway  ISOTAF12 (Homo sapiens) RGD 
Taf13RatRNA polymerase II transcription initiation pathway  ISOTAF13 (Homo sapiens) RGD 
Taf13MouseRNA polymerase II transcription initiation pathway  ISOTAF13 (Homo sapiens) RGD 
Taf15RatRNA polymerase II transcription initiation pathway  ISOTAF15 (Homo sapiens) RGD 
Taf15MouseRNA polymerase II transcription initiation pathway  ISOTAF15 (Homo sapiens) RGD 
Taf2RatRNA polymerase II transcription initiation pathway  ISOTAF2 (Homo sapiens) RGD 
Taf2MouseRNA polymerase II transcription initiation pathway  ISOTAF2 (Homo sapiens) RGD 
Taf3MouseRNA polymerase II transcription initiation pathway  ISOTAF3 (Homo sapiens) RGD 
Taf3RatRNA polymerase II transcription initiation pathway  ISOTAF3 (Homo sapiens) RGD 
Taf4RatRNA polymerase II transcription initiation pathway  ISOTAF4 (Homo sapiens) RGD 
Taf4MouseRNA polymerase II transcription initiation pathway  ISOTAF4 (Homo sapiens) RGD 
Taf5RatRNA polymerase II transcription initiation pathway  ISOTAF5 (Homo sapiens) RGD 
Taf5MouseRNA polymerase II transcription initiation pathway  ISOTAF5 (Homo sapiens) RGD 
Taf6RatRNA polymerase II transcription initiation pathway  ISOTAF6 (Homo sapiens) RGD 
Taf6MouseRNA polymerase II transcription initiation pathway  ISOTAF6 (Homo sapiens) RGD 
Taf7RatRNA polymerase II transcription initiation pathway  ISOTAF7 (Homo sapiens) RGD 
Taf7MouseRNA polymerase II transcription initiation pathway  ISOTAF7 (Homo sapiens) RGD 
Taf8RatRNA polymerase II transcription initiation pathway  ISOTAF8 (Homo sapiens) RGD 
Taf8MouseRNA polymerase II transcription initiation pathway  ISOTAF8 (Homo sapiens) RGD 
Taf9RatRNA polymerase II transcription initiation pathway  ISOTAF9 (Homo sapiens) RGD 
Taf9MouseRNA polymerase II transcription initiation pathway  ISOTAF9 (Homo sapiens) RGD 
TbpRatRNA polymerase II transcription initiation pathway  ISOTBP (Homo sapiens) RGD 
TbpMouseRNA polymerase II transcription initiation pathway  ISOTBP (Homo sapiens) RGD 
Objects Annotated

Genes (Rattus norvegicus)
Taf1  (TATA-box binding protein associated factor 1)
Taf10  (TATA-box binding protein associated factor 10)
Taf11  (TATA-box binding protein associated factor 11)
Taf12  (TATA-box binding protein associated factor 12)
Taf13  (TATA-box binding protein associated factor 13)
Taf15  (TATA-box binding protein associated factor 15)
Taf2  (TATA-box binding protein associated factor 2)
Taf3  (TATA-box binding protein associated factor 3)
Taf4  (TATA-box binding protein associated factor 4)
Taf5  (TATA-box binding protein associated factor 5)
Taf6  (TATA-box binding protein associated factor 6)
Taf7  (TATA-box binding protein associated factor 7)
Taf8  (TATA-box binding protein associated factor 8)
Taf9  (TATA-box binding protein associated factor 9)
Tbp  (TATA box binding protein)

Genes (Mus musculus)
Taf1  (TATA-box binding protein associated factor 1)
Taf10  (TATA-box binding protein associated factor 10)
Taf11  (TATA-box binding protein associated factor 11)
Taf12  (TATA-box binding protein associated factor 12)
Taf13  (TATA-box binding protein associated factor 13)
Taf15  (TATA-box binding protein associated factor 15)
Taf2  (TATA-box binding protein associated factor 2)
Taf3  (TATA-box binding protein associated factor 3)
Taf4  (TATA-box binding protein associated factor 4)
Taf5  (TATA-box binding protein associated factor 5)
Taf6  (TATA-box binding protein associated factor 6)
Taf7  (TATA-box binding protein associated factor 7)
Taf8  (TATA-box binding protein associated factor 8)
Taf9  (TATA-box binding protein associated factor 9)
Tbp  (TATA box binding protein)

Genes (Homo sapiens)
TAF1  (TATA-box binding protein associated factor 1)
TAF10  (TATA-box binding protein associated factor 10)
TAF11  (TATA-box binding protein associated factor 11)
TAF12  (TATA-box binding protein associated factor 12)
TAF13  (TATA-box binding protein associated factor 13)
TAF15  (TATA-box binding protein associated factor 15)
TAF2  (TATA-box binding protein associated factor 2)
TAF3  (TATA-box binding protein associated factor 3)
TAF4  (TATA-box binding protein associated factor 4)
TAF5  (TATA-box binding protein associated factor 5)
TAF6  (TATA-box binding protein associated factor 6)
TAF7  (TATA-box binding protein associated factor 7)
TAF8  (TATA-box binding protein associated factor 8)
TAF9  (TATA-box binding protein associated factor 9)
TBP  (TATA-box binding protein)


Additional Information