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SAGA-associated factor 29 (29 kDa SAGA-associated factor) (SAGA histone acetyltransferase complex 29 kDa subunit)

 SGF29_YEAST             Reviewed;         259 AA.
P25554; D6VR02; P87008;
01-MAY-1992, integrated into UniProtKB/Swiss-Prot.
30-MAY-2000, sequence version 2.
10-OCT-2018, entry version 156.
RecName: Full=SAGA-associated factor 29;
AltName: Full=29 kDa SAGA-associated factor;
AltName: Full=SAGA histone acetyltransferase complex 29 kDa subunit;
Name=SGF29; OrderedLocusNames=YCL010C; ORFNames=YCL10C;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=1574125; DOI=10.1038/357038a0;
Oliver S.G., van der Aart Q.J.M., Agostoni-Carbone M.L., Aigle M.,
Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J.P.G.,
Benit P., Berben G., Bergantino E., Biteau N., Bolle P.-A.,
Bolotin-Fukuhara M., Brown A., Brown A.J.P., Buhler J.-M., Carcano C.,
Carignani G., Cederberg H., Chanet R., Contreras R., Crouzet M.,
Daignan-Fornier B., Defoor E., Delgado M.D., Demolder J., Doira C.,
Dubois E., Dujon B., Duesterhoeft A., Erdmann D., Esteban M.,
Fabre F., Fairhead C., Faye G., Feldmann H., Fiers W.,
Francingues-Gaillard M.-C., Franco L., Frontali L., Fukuhara H.,
Fuller L.J., Galland P., Gent M.E., Gigot D., Gilliquet V.,
Glansdorff N., Goffeau A., Grenson M., Grisanti P., Grivell L.A.,
de Haan M., Haasemann M., Hatat D., Hoenicka J., Hegemann J.H.,
Herbert C.J., Hilger F., Hohmann S., Hollenberg C.P., Huse K.,
Iborra F., Indge K.J., Isono K., Jacq C., Jacquet M., James C.M.,
Jauniaux J.-C., Jia Y., Jimenez A., Kelly A., Kleinhans U., Kreisl P.,
Lanfranchi G., Lewis C., van der Linden C.G., Lucchini G.,
Lutzenkirchen K., Maat M.J., Mallet L., Mannhaupt G., Martegani E.,
Mathieu A., Maurer C.T.C., McConnell D., McKee R.A., Messenguy F.,
Mewes H.-W., Molemans F., Montague M.A., Muzi Falconi M., Navas L.,
Newlon C.S., Noone D., Pallier C., Panzeri L., Pearson B.M., Perea J.,
Philippsen P., Pierard A., Planta R.J., Plevani P., Poetsch B.,
Pohl F.M., Purnelle B., Ramezani Rad M., Rasmussen S.W., Raynal A.,
Remacha M.A., Richterich P., Roberts A.B., Rodriguez F., Sanz E.,
Schaaff-Gerstenschlaeger I., Scherens B., Schweitzer B., Shu Y.,
Skala J., Slonimski P.P., Sor F., Soustelle C., Spiegelberg R.,
Stateva L.I., Steensma H.Y., Steiner S., Thierry A., Thireos G.,
Tzermia M., Urrestarazu L.A., Valle G., Vetter I.,
van Vliet-Reedijk J.C., Voet M., Volckaert G., Vreken P., Wang H.,
Warmington J.R., von Wettstein D., Wicksteed B.L., Wilson C.,
Wurst H., Xu G., Yoshikawa A., Zimmermann F.K., Sgouros J.G.;
"The complete DNA sequence of yeast chromosome III.";
Nature 357:38-46(1992).
[2]
SEQUENCE REVISION.
Gromadka R.;
Submitted (JAN-1996) to the EMBL/GenBank/DDBJ databases.
[3]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[4]
FUNCTION IN HISTONE ACETYLATION AT THE SAGA COMPLEX.
PubMed=10026213; DOI=10.1074/jbc.274.9.5895;
Grant P.A., Eberharter A., John S., Cook R.G., Turner B.M.,
Workman J.L.;
"Expanded lysine acetylation specificity of Gcn5 in native
complexes.";
J. Biol. Chem. 274:5895-5900(1999).
[5]
IDENTIFICATION IN THE SAGA COMPLEX.
PubMed=12052880; DOI=10.1128/MCB.22.13.4723-4738.2002;
Sanders S.L., Jennings J., Canutescu A., Link A.J., Weil P.A.;
"Proteomics of the eukaryotic transcription machinery: identification
of proteins associated with components of yeast TFIID by
multidimensional mass spectrometry.";
Mol. Cell. Biol. 22:4723-4738(2002).
[6]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[7]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-139, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=YAL6B;
PubMed=15665377; DOI=10.1074/mcp.M400219-MCP200;
Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J.,
Mann M., Jensen O.N.;
"Quantitative phosphoproteomics applied to the yeast pheromone
signaling pathway.";
Mol. Cell. Proteomics 4:310-327(2005).
[8]
FUNCTION, AND IDENTIFICATION IN THE SLIK COMPLEX.
PubMed=15647753; DOI=10.1038/nature03242;
Pray-Grant M.G., Daniel J.A., Schieltz D., Yates J.R. III, Grant P.A.;
"Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-
dependent acetylation.";
Nature 433:434-438(2005).
[9]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-139, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ADR376;
PubMed=17330950; DOI=10.1021/pr060559j;
Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
Elias J.E., Gygi S.P.;
"Large-scale phosphorylation analysis of alpha-factor-arrested
Saccharomyces cerevisiae.";
J. Proteome Res. 6:1190-1197(2007).
[10]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-139, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=18407956; DOI=10.1074/mcp.M700468-MCP200;
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
"A multidimensional chromatography technology for in-depth
phosphoproteome analysis.";
Mol. Cell. Proteomics 7:1389-1396(2008).
[11]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-139, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19779198; DOI=10.1126/science.1172867;
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
"Global analysis of Cdk1 substrate phosphorylation sites provides
insights into evolution.";
Science 325:1682-1686(2009).
[12]
3D-STRUCTURE MODELING OF THE SAGA COMPLEX.
PubMed=15260971; DOI=10.1016/j.molcel.2004.06.005;
Wu P.Y., Ruhlmann C., Winston F., Schultz P.;
"Molecular architecture of the S. cerevisiae SAGA complex.";
Mol. Cell 15:199-208(2004).
[13]
X-RAY CRYSTALLOGRAPHY (1.48 ANGSTROMS) OF 113-259 IN COMPLEX WITH
H3K4ME3 PEPTIDE, INTERACTION WITH H3K4ME2 AND H3K4ME3, FUNCTION,
DOMAIN, AND MUTAGENESIS OF ASP-163; GLU-165; TYR-205; THR-210; TYR-212
AND PHE-229.
PubMed=21685874; DOI=10.1038/emboj.2011.193;
Bian C., Xu C., Ruan J., Lee K.K., Burke T.L., Tempel W., Barsyte D.,
Li J., Wu M., Zhou B.O., Fleharty B.E., Paulson A., Allali-Hassani A.,
Zhou J.Q., Mer G., Grant P.A., Workman J.L., Zang J., Min J.;
"Sgf29 binds histone H3K4me2/3 and is required for SAGA complex
recruitment and histone H3 acetylation.";
EMBO J. 30:2829-2842(2011).
[14]
FUNCTION.
PubMed=24307402; DOI=10.1093/jb/mvt108;
Kamata K., Goswami G., Kashio S., Urano T., Nakagawa R., Uchida H.,
Oki M.;
"The N-terminus and Tudor domains of Sgf29 are important for its
heterochromatin boundary formation function.";
J. Biochem. 155:159-171(2014).
-!- FUNCTION: Chromatin reader component of the transcription
regulatory histone acetylation (HAT) complexes SAGA and SLIK
(PubMed:10026213, PubMed:15647753, PubMed:21685874,
PubMed:24307402). In the SAGA complex, SGF29 specifically
recognizes and binds methylated 'Lys-4' of histone H3 (H3K4me),
with a preference for trimethylated form (H3K4me3)
(PubMed:21685874). SGF29 is also required for heterochromatin
boundary formation function (PubMed:24307402). 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
(PubMed:10026213). 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) (PubMed:10026213). SAGA acetylates
nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac,
H3K18ac and H3K23ac). SAGA interacts with DNA via upstream
activating sequences (UASs) (PubMed:10026213). SLIK is proposed to
have partly overlapping functions with SAGA (PubMed:15647753). It
preferentially acetylates methylated histone H3, at least after
activation at the GAL1-10 locus (PubMed:15647753).
{ECO:0000269|PubMed:10026213, ECO:0000269|PubMed:15647753,
ECO:0000269|PubMed:21685874, ECO:0000269|PubMed:24307402}.
-!- SUBUNIT: Component of the 1.8 MDa SAGA complex, which consists of
at least of 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. Interacts with dimethylated and trimethylated 'Lys-4'
of histone H3 (H3K4me2 and H3K4me3), with a preference for the
trimethylated form (H3K4me3). 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.
{ECO:0000269|PubMed:12052880, ECO:0000269|PubMed:15647753,
ECO:0000269|PubMed:21685874}.
-!- INTERACTION:
Q12060:HFI1; NbExp=9; IntAct=EBI-21678, EBI-8287;
P68431:HIST1H3D (xeno); NbExp=11; IntAct=EBI-21678, EBI-79722;
P32494:NGG1; NbExp=5; IntAct=EBI-21678, EBI-2192;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
-!- DOMAIN: The SGF29 C-terminal (also named tudor-like) domain
mediates binding to methylated 'Lys-4' of histone H3 (H3K4me).
{ECO:0000255|PROSITE-ProRule:PRU00851,
ECO:0000269|PubMed:21685874}.
-!- MISCELLANEOUS: Present with 1750 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the SGF29 family. {ECO:0000255|PROSITE-
ProRule:PRU00851}.
-----------------------------------------------------------------------
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EMBL; X59720; CAA42349.1; -; Genomic_DNA.
EMBL; BK006937; DAA07471.1; -; Genomic_DNA.
PIR; S74287; S74287.
RefSeq; NP_009917.1; NM_001178659.1.
PDB; 3MP1; X-ray; 2.60 A; A=111-259.
PDB; 3MP6; X-ray; 1.48 A; A=111-259.
PDB; 3MP8; X-ray; 1.92 A; A=111-259.
PDBsum; 3MP1; -.
PDBsum; 3MP6; -.
PDBsum; 3MP8; -.
ProteinModelPortal; P25554; -.
SMR; P25554; -.
BioGrid; 30971; 565.
ComplexPortal; CPX-656; SAGA complex.
DIP; DIP-4871N; -.
IntAct; P25554; 93.
MINT; P25554; -.
STRING; 4932.YCL010C; -.
iPTMnet; P25554; -.
MaxQB; P25554; -.
PaxDb; P25554; -.
PRIDE; P25554; -.
EnsemblFungi; CAA42349; CAA42349; CAA42349.
EnsemblFungi; YCL010C; YCL010C; YCL010C.
GeneID; 850347; -.
KEGG; sce:YCL010C; -.
EuPathDB; FungiDB:YCL010C; -.
SGD; S000000516; SGF29.
HOGENOM; HOG000248873; -.
InParanoid; P25554; -.
KO; K11364; -.
OMA; EEWIQCE; -.
OrthoDB; EOG092C3A9R; -.
BioCyc; YEAST:G3O-29279-MONOMER; -.
EvolutionaryTrace; P25554; -.
PRO; PR:P25554; -.
Proteomes; UP000002311; Chromosome III.
GO; GO:0005671; C:Ada2/Gcn5/Ada3 transcription activator complex; IMP:SGD.
GO; GO:0000124; C:SAGA complex; IDA:SGD.
GO; GO:0035064; F:methylated histone binding; IDA:SGD.
GO; GO:0001135; F:RNA polymerase II transcription factor recruiting activity; IMP:SGD.
GO; GO:0034613; P:cellular protein localization; IMP:SGD.
GO; GO:0034629; P:cellular protein-containing complex localization; IMP:SGD.
GO; GO:0070868; P:heterochromatin organization involved in chromatin silencing; IMP:SGD.
GO; GO:0044154; P:histone H3-K14 acetylation; IMP:SGD.
GO; GO:0043971; P:histone H3-K18 acetylation; IMP:SGD.
GO; GO:0043970; P:histone H3-K9 acetylation; IMP:SGD.
GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IMP:SGD.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
InterPro; IPR037802; SGF29.
InterPro; IPR010750; SGF29_tudor-like_dom.
PANTHER; PTHR21539; PTHR21539; 1.
Pfam; PF07039; DUF1325; 1.
PROSITE; PS51518; SGF29_C; 1.
1: Evidence at protein level;
3D-structure; Chromatin regulator; Complete proteome; Nucleus;
Phosphoprotein; Reference proteome; Transcription;
Transcription regulation.
CHAIN 1 259 SAGA-associated factor 29.
/FTId=PRO_0000202539.
DOMAIN 121 255 SGF29 C-terminal. {ECO:0000255|PROSITE-
ProRule:PRU00851}.
REGION 163 165 Histone H3K4me3 N-terminus binding.
{ECO:0000269|PubMed:21685874}.
REGION 207 210 Histone H3K4me3 N-terminus binding.
{ECO:0000269|PubMed:21685874}.
REGION 229 232 Histone H3K4me3 binding.
{ECO:0000269|PubMed:21685874}.
BINDING 205 205 Histone H3K4me3.
{ECO:0000269|PubMed:21685874}.
BINDING 212 212 Histone H3K4me3.
{ECO:0000269|PubMed:21685874}.
MOD_RES 139 139 Phosphoserine.
{ECO:0000244|PubMed:15665377,
ECO:0000244|PubMed:17330950,
ECO:0000244|PubMed:18407956,
ECO:0000244|PubMed:19779198}.
MUTAGEN 163 163 D->A: Reduces histone H3 acetylation.
{ECO:0000269|PubMed:21685874}.
MUTAGEN 165 165 E->A: Reduces histone H3 acetylation.
{ECO:0000269|PubMed:21685874}.
MUTAGEN 205 205 Y->A: Reduces histone H3 acetylation.
{ECO:0000269|PubMed:21685874}.
MUTAGEN 210 210 T->A: Reduces histone H3 acetylation.
{ECO:0000269|PubMed:21685874}.
MUTAGEN 212 212 Y->A: Reduces histone H3 acetylation.
{ECO:0000269|PubMed:21685874}.
MUTAGEN 229 229 F->A: Reduces histone H3 acetylation.
{ECO:0000269|PubMed:21685874}.
STRAND 105 107 {ECO:0000244|PDB:3MP1}.
STRAND 118 120 {ECO:0000244|PDB:3MP6}.
STRAND 130 133 {ECO:0000244|PDB:3MP6}.
TURN 140 142 {ECO:0000244|PDB:3MP8}.
STRAND 144 153 {ECO:0000244|PDB:3MP6}.
TURN 154 157 {ECO:0000244|PDB:3MP6}.
STRAND 158 163 {ECO:0000244|PDB:3MP6}.
STRAND 174 178 {ECO:0000244|PDB:3MP6}.
HELIX 180 182 {ECO:0000244|PDB:3MP6}.
STRAND 183 186 {ECO:0000244|PDB:3MP6}.
STRAND 200 204 {ECO:0000244|PDB:3MP6}.
STRAND 209 219 {ECO:0000244|PDB:3MP6}.
STRAND 225 229 {ECO:0000244|PDB:3MP6}.
STRAND 232 234 {ECO:0000244|PDB:3MP8}.
STRAND 239 241 {ECO:0000244|PDB:3MP6}.
HELIX 243 245 {ECO:0000244|PDB:3MP6}.
STRAND 246 248 {ECO:0000244|PDB:3MP6}.
HELIX 250 253 {ECO:0000244|PDB:3MP6}.
SEQUENCE 259 AA; 29381 MW; 4DD51E36BB01C073 CRC64;
MDGYWDVVVS SLQDIYNANE VIPFDDELQT KKLNFLNMSK DQLQLHLNTF QEHMENVNRV
HRILDNVRSN LSLMLNQSRE EKSEENTEDA EEGEGTRMAL SQGKKAVGKV GRSYWTSEYN
PNAPILVGSE VAYKPRRGSA DGEWIQCEVL KVVADGTRFE VRDPEPDELG NSGKVYKCNR
KELLLIPPGF PTKNYPPGTK VLARYPETTT FYPAIVIGTK RDGTCRLRFD GEEEVDKETE
VTRRLVLPSP TALANLARK


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