Transcription initiation factor TFIID subunit 9 - Saccharomyces cerevisiae (Baker's yeast)

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Reviewed, UniProtKB/Swiss-Prot Q05027 (TAF9_YEAST)

Last modified November 24, 2009. Version 81. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Transcription initiation factor TFIID subunit 9
Alternative name(s):
    TBP-associated factor 9
    TBP-associated factor 17 kDa
    TAFII-17
    TAFII20

Gene names

Name:	TAF9
Synonyms:	TAF17
Ordered Locus Names:	YMR236W
ORF Names:	YM9959.18

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

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Protein attributes

Sequence length	157 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Functions as a component of the DNA-binding general transcription factor complex TFIID and the transcription regulatory histone acetylation (HAT) complex SAGA and SLIK. Binding of TFIID to a promoter (with or without TATA element) is the initial step in preinitiation complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modification (histone acetylation by TAF1), facilitation of DNA opening and initiation of transcription. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3, and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus. Ref.2 Ref.3 Ref.4 Ref.5 Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 Ref.12
Subunit structure	In TFIID, TAF9 heterodimerizes with TAF6, forming ultimately an octamer consisting of a TAF6/TAF9 heterotetramer core flanked by TAF4/TAF12 dimers on either side, similar to the histone H2A/H2B/H3/H4 octamer. The 1.2 MDa TFIID complex is composed of TATA binding protein (TBP) and the 14 TBP-associated factors. One copy of each TAF1, TAF2, TAF3, TAF7, TAF8, TAF11, TAF13, two copies of each TAF4, TAF5, TAF6, TAF9, TAF10, TAF12, and three copies of TAF14. Component of the 1.8 MDa SAGA complex, which consists of at least TRA1, CHD1, SPT7, TAF5, ADA3, SGF73, SPT20/ADA5, SPT8, TAF12, TAF6, HFI1/ADA1, UBP8, GCN5, ADA2, SPT3, SGF29, TAF10, TAF9, SGF11 and SUS1. TAF5, TAF6, TAF9, TAF19, TAF12 and ADA1 seem to be present in 2 copies. SAGA is built of 5 distinct domains with specialized functions. Domain I (containing TRA1) probably represents the activator interaction surface. Domain II (containing TAF5 and TAF6, and probably TAF9 and TAF10), domain III (containing GCN5, TAF10, SPT7, TAF5 and ADA1, and probably ADA2, ADA3 and TAF12), and domain IV (containing HFI1/ADA1 and TAF6, and probably TAF9) are believed to play primarily an architectural role. Domain III also harbors the HAT activity. Domain V (containing SPT3 and SPT20, and probably SPT8) represents the TBP-interacting module, which may be associated transiently with SAGA. Component of the SLIK complex, which consists of at least TRA1, CHD1, SPT7, TAF5, ADA3, SPT20, RTG2, TAF12, TAF6, HFI1, UBP8, GCN5, ADA2, SPT3, SGF29, TAF10 AND TAF9. Ref.5
Subcellular location	Nucleus.
Miscellaneous	Present with 7000 molecules/cell in log phase SD medium. Ref.14
Sequence similarities	Belongs to the TAF9 family. Contains 1 histone-fold domain.

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Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
PTM	Phosphoprotein
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	RNA polymerase II transcriptional preinitiation complex assembly Inferred from mutant phenotype. Source: SGD gene-specific transcription from RNA polymerase II promoter Inferred from mutant phenotype. Source: SGD general transcription from RNA polymerase II promoter Ref.10 Inferred from direct assay. Source: SGD histone acetylation Ref.3 Inferred from direct assay. Source: SGD regulation of transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	SAGA complex Ref.3 Inferred from direct assay. Source: SGD SLIK (SAGA-like) complex Ref.11 Inferred from direct assay. Source: SGD transcription factor TFIID complex Ref.5 Inferred from direct assay. Source: SGD
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro chromatin binding Inferred from direct assay. Source: SGD general RNA polymerase II transcription factor activity Ref.10 Inferred from direct assay. Source: SGD identical protein binding Ref.10 Inferred from physical interaction. Source: IntAct protein complex scaffold Inferred from mutant phenotype. Source: SGD specific RNA polymerase II transcription factor activity Inferred from mutant phenotype. Source: SGD
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct
itself		1	EBI-27500,EBI-27500
ADE2	P21264	1	EBI-27500,EBI-14252
TAF6	P53040	1	EBI-27500,EBI-18876

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 157

157

Transcription initiation factor TFIID subunit 9

PRO_0000118896

Regions

Domain

30 – 97

Histone-fold

Amino acid modifications

Modified residue

Phosphoserine Ref.17

Modified residue

Phosphoserine Ref.17

Modified residue

Phosphothreonine Ref.17

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Sequences

Sequence

Length

Mass (Da)

Tools

Q05027-1 [UniParc].

Last modified November 1, 1997. Version 1.
Checksum: D1C97EDDCA468EC5
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FASTA

157

17,315

        10         20         30         40         50         60 
MNGGGKNVLN KNSVGSVSEV GPDSTQEETP RDVRLLHLLL ASQSIHQYED QVPLQLMDFA 

        70         80         90        100        110        120 
HRYTQGVLKD ALVYNDYAGS GNSAGSGLGV EDIRLAIAAR TQYQFKPTAP KELMLQLAAE 

       130        140        150 
RNKKALPQVM GTWGVRLPPE KYCLTAKEWD LEDPKSM

« Hide

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII." Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T., Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K., Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P. Barrell B.G. Nature 387:90-93(1997) [PubMed: 9169872] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[2]	"Human TAF(II)28 and TAF(II)18 interact through a histone fold encoded by atypical evolutionary conserved motifs also found in the SPT3 family." Birck C., Poch O., Romier C., Ruff M., Mengus G., Lavigne A.C., Davidson I., Moras D. Cell 94:239-249(1998) [PubMed: 9695952] [Abstract] Cited for: FUNCTION, TAF-TAF INTERACTION THROUGH HISTONE-FOLD DOMAIN.
[3]	"A subset of TAF(II)s are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation." Grant P.A., Schieltz D., Pray-Grant M.G., Steger D.J., Reese J.C., Yates J.R. III, Workman J.L. Cell 94:45-53(1998) [PubMed: 9674426] [Abstract] Cited for: FUNCTION, IDENTIFICATION IN THE SAGA COMPLEX, MASS SPECTROMETRY.
[4]	"Expanded lysine acetylation specificity of Gcn5 in native complexes." Grant P.A., Eberharter A., John S., Cook R.G., Turner B.M., Workman J.L. J. Biol. Chem. 274:5895-5900(1999) [PubMed: 10026213] [Abstract] Cited for: FUNCTION IN HISTONE ACETYLATION AT THE SAGA COMPLEX.
[5]	"Identification of two novel TAF subunits of the yeast Saccharomyces cerevisiae TFIID complex." Sanders S.L., Weil P.A. J. Biol. Chem. 275:13895-13900(2000) [PubMed: 10788514] [Abstract] Cited for: FUNCTION, SUBUNIT.
[6]	"Histone folds mediate selective heterodimerization of yeast TAF(II)25 with TFIID components yTAF(II)47 and yTAF(II)65 and with SAGA component ySPT7." Gangloff Y.G., Sanders S.L., Romier C., Kirschner D.B., Weil P.A., Tora L., Davidson I. Mol. Cell. Biol. 21:1841-1853(2001) [PubMed: 11238921] [Abstract] Cited for: FUNCTION, INTERACTION IN TFIID AND SAGA.
[7]	"The histone fold is a key structural motif of transcription factor TFIID." Gangloff Y.G., Romier C., Thuault S., Werten S., Davidson I. Trends Biochem. Sci. 26:250-257(2001) [PubMed: 11295558] [Abstract] Cited for: FUNCTION, HISTONE-FOLD DOMAIN CHARACTERIZATION.
[8]	"A histone fold TAF octamer within the yeast TFIID transcriptional coactivator." Selleck W., Howley R., Fang Q., Podolny V., Fried M.G., Buratowski S., Tan S. Nat. Struct. Biol. 8:695-700(2001) [PubMed: 11473260] [Abstract] Cited for: FUNCTION, TAF OCTAMER FORMATION.
[9]	"Proteomics of the eukaryotic transcription machinery: identification of proteins associated with components of yeast TFIID by multidimensional mass spectrometry." Sanders S.L., Jennings J., Canutescu A., Link A.J., Weil P.A. Mol. Cell. Biol. 22:4723-4738(2002) [PubMed: 12052880] [Abstract] Cited for: FUNCTION, IDENTIFICATION IN THE SAGA COMPLEX.
[10]	"Molecular characterization of Saccharomyces cerevisiae TFIID." Sanders S.L., Garbett K.A., Weil P.A. Mol. Cell. Biol. 22:6000-6013(2002) [PubMed: 12138208] [Abstract] Cited for: FUNCTION, TFIID STOICHIOMETRY.
[11]	"The novel SLIK histone acetyltransferase complex functions in the yeast retrograde response pathway." Pray-Grant M.G., Schieltz D., McMahon S.J., Wood J.M., Kennedy E.L., Cook R.G., Workman J.L., Yates J.R. III, Grant P.A. Mol. Cell. Biol. 22:8774-8786(2002) [PubMed: 12446794] [Abstract] Cited for: IDENTIFICATION IN THE SLIK COMPLEX.
[12]	"Multi-protein complexes in eukaryotic gene transcription." Martinez E. Plant Mol. Biol. 50:925-947(2002) [PubMed: 12516863] [Abstract] Cited for: FUNCTION.
[13]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed: 14562095] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[14]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[15]	"Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation." Pray-Grant M.G., Daniel J.A., Schieltz D., Yates J.R. III, Grant P.A. Nature 433:434-438(2005) [PubMed: 15647753] [Abstract] Cited for: IDENTIFICATION IN THE SLIK COMPLEX.
[16]	"Mapping histone fold TAFs within yeast TFIID." Leurent C., Sanders S.L., Ruhlmann C., Mallouh V., Weil P.A., Kirschner D.B., Tora L., Schultz P. EMBO J. 21:3424-3433(2002) [PubMed: 12093743] [Abstract] Cited for: 3D-STRUCTURE, ELECTRON MICROSCOPY OF TFIID.
[17]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-13; SER-18 AND THR-25, MASS SPECTROMETRY.
[18]	"Molecular architecture of the S. cerevisiae SAGA complex." Wu P.Y., Ruhlmann C., Winston F., Schultz P. Mol. Cell 15:199-208(2004) [PubMed: 15260971] [Abstract] Cited for: 3D-STRUCTURE MODELING OF THE SAGA COMPLEX.
+	Additional computationally mapped references.

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Cross-references

Sequence databases
	Z49939 Genomic DNA. Translation: CAA90207.1.
PIR	S57603.
RefSeq	NP_013963.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
DIP	DIP:925N.
IntAct	Q05027. 32 interactions.
STRING	Q05027.
Proteomic databases
PeptideAtlas	Q05027.
Genome annotation databases
Ensembl	YMR236W; YMR236W; YMR236W; Saccharomyces cerevisiae. [Genome view]
GeneID	855276.
KEGG	sce:YMR236W.
NMPDR	fig\|4932.3.peg.5017.
Organism-specific databases
CYGD	YMR236w.
SGD	S000004849. TAF9.
Phylogenomic databases
HOGENOM	Q05027.
OMA	QFKPTAP
OrthoDB	EOG9XD57F
Gene expression databases
ArrayExpress	Q05027.
Genevestigator	Q05027.
GermOnline	YMR236W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR009072. Histone-fold. IPR003162. TFIID-31. [Graphical view]
Gene3D	G3DSA:1.10.20.10. Histone-fold. 1 hit.
PANTHER	PTHR12075. TFIID-31. 1 hit.
Pfam	PF02291. TFIID-31kDa. 1 hit. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	978900.

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Entry information

Entry name

TAF9_YEAST

Accession

Primary (citable) accession number: Q05027

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1997
Last modified:	November 24, 2009
This is version 81 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)

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Relevant documents

SIMILARITY comments

Index of protein domains and families

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome XIII

Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Amino acid modifications

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other Resources

Entry information

Relevant documents