SGF29_YEAST
ID SGF29_YEAST Reviewed; 259 AA.
AC P25554; D6VR02; P87008;
DT 01-MAY-1992, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2000, sequence version 2.
DT 03-AUG-2022, entry version 179.
DE RecName: Full=SAGA-associated factor 29;
DE AltName: Full=29 kDa SAGA-associated factor;
DE AltName: Full=SAGA histone acetyltransferase complex 29 kDa subunit;
GN Name=SGF29; OrderedLocusNames=YCL010C; ORFNames=YCL10C;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=1574125; DOI=10.1038/357038a0;
RA Oliver S.G., van der Aart Q.J.M., Agostoni-Carbone M.L., Aigle M.,
RA Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J.P.G.,
RA Benit P., Berben G., Bergantino E., Biteau N., Bolle P.-A.,
RA Bolotin-Fukuhara M., Brown A., Brown A.J.P., Buhler J.-M., Carcano C.,
RA Carignani G., Cederberg H., Chanet R., Contreras R., Crouzet M.,
RA Daignan-Fornier B., Defoor E., Delgado M.D., Demolder J., Doira C.,
RA Dubois E., Dujon B., Duesterhoeft A., Erdmann D., Esteban M., Fabre F.,
RA Fairhead C., Faye G., Feldmann H., Fiers W., Francingues-Gaillard M.-C.,
RA Franco L., Frontali L., Fukuhara H., Fuller L.J., Galland P., Gent M.E.,
RA Gigot D., Gilliquet V., Glansdorff N., Goffeau A., Grenson M., Grisanti P.,
RA Grivell L.A., de Haan M., Haasemann M., Hatat D., Hoenicka J.,
RA Hegemann J.H., Herbert C.J., Hilger F., Hohmann S., Hollenberg C.P.,
RA Huse K., Iborra F., Indge K.J., Isono K., Jacq C., Jacquet M., James C.M.,
RA Jauniaux J.-C., Jia Y., Jimenez A., Kelly A., Kleinhans U., Kreisl P.,
RA Lanfranchi G., Lewis C., van der Linden C.G., Lucchini G.,
RA Lutzenkirchen K., Maat M.J., Mallet L., Mannhaupt G., Martegani E.,
RA Mathieu A., Maurer C.T.C., McConnell D., McKee R.A., Messenguy F.,
RA Mewes H.-W., Molemans F., Montague M.A., Muzi Falconi M., Navas L.,
RA Newlon C.S., Noone D., Pallier C., Panzeri L., Pearson B.M., Perea J.,
RA Philippsen P., Pierard A., Planta R.J., Plevani P., Poetsch B., Pohl F.M.,
RA Purnelle B., Ramezani Rad M., Rasmussen S.W., Raynal A., Remacha M.A.,
RA Richterich P., Roberts A.B., Rodriguez F., Sanz E.,
RA Schaaff-Gerstenschlaeger I., Scherens B., Schweitzer B., Shu Y., Skala J.,
RA Slonimski P.P., Sor F., Soustelle C., Spiegelberg R., Stateva L.I.,
RA Steensma H.Y., Steiner S., Thierry A., Thireos G., Tzermia M.,
RA Urrestarazu L.A., Valle G., Vetter I., van Vliet-Reedijk J.C., Voet M.,
RA Volckaert G., Vreken P., Wang H., Warmington J.R., von Wettstein D.,
RA Wicksteed B.L., Wilson C., Wurst H., Xu G., Yoshikawa A., Zimmermann F.K.,
RA Sgouros J.G.;
RT "The complete DNA sequence of yeast chromosome III.";
RL Nature 357:38-46(1992).
RN [2]
RP SEQUENCE REVISION.
RA Gromadka R.;
RL Submitted (JAN-1996) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP FUNCTION IN HISTONE ACETYLATION AT THE SAGA COMPLEX.
RX PubMed=10026213; DOI=10.1074/jbc.274.9.5895;
RA Grant P.A., Eberharter A., John S., Cook R.G., Turner B.M., Workman J.L.;
RT "Expanded lysine acetylation specificity of Gcn5 in native complexes.";
RL J. Biol. Chem. 274:5895-5900(1999).
RN [5]
RP IDENTIFICATION IN THE SAGA COMPLEX.
RX PubMed=12052880; DOI=10.1128/mcb.22.13.4723-4738.2002;
RA Sanders S.L., Jennings J., Canutescu A., Link A.J., Weil P.A.;
RT "Proteomics of the eukaryotic transcription machinery: identification of
RT proteins associated with components of yeast TFIID by multidimensional mass
RT spectrometry.";
RL Mol. Cell. Biol. 22:4723-4738(2002).
RN [6]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-139, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=YAL6B;
RX PubMed=15665377; DOI=10.1074/mcp.m400219-mcp200;
RA Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M.,
RA Jensen O.N.;
RT "Quantitative phosphoproteomics applied to the yeast pheromone signaling
RT pathway.";
RL Mol. Cell. Proteomics 4:310-327(2005).
RN [8]
RP FUNCTION, AND IDENTIFICATION IN THE SLIK COMPLEX.
RX PubMed=15647753; DOI=10.1038/nature03242;
RA Pray-Grant M.G., Daniel J.A., Schieltz D., Yates J.R. III, Grant P.A.;
RT "Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-
RT dependent acetylation.";
RL Nature 433:434-438(2005).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-139, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-139, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-139, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [12]
RP 3D-STRUCTURE MODELING OF THE SAGA COMPLEX.
RX PubMed=15260971; DOI=10.1016/j.molcel.2004.06.005;
RA Wu P.Y., Ruhlmann C., Winston F., Schultz P.;
RT "Molecular architecture of the S. cerevisiae SAGA complex.";
RL Mol. Cell 15:199-208(2004).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (1.48 ANGSTROMS) OF 113-259 IN COMPLEX WITH H3K4ME3
RP PEPTIDE, INTERACTION WITH H3K4ME2 AND H3K4ME3, FUNCTION, DOMAIN, AND
RP MUTAGENESIS OF ASP-163; GLU-165; TYR-205; THR-210; TYR-212 AND PHE-229.
RX PubMed=21685874; DOI=10.1038/emboj.2011.193;
RA Bian C., Xu C., Ruan J., Lee K.K., Burke T.L., Tempel W., Barsyte D.,
RA Li J., Wu M., Zhou B.O., Fleharty B.E., Paulson A., Allali-Hassani A.,
RA Zhou J.Q., Mer G., Grant P.A., Workman J.L., Zang J., Min J.;
RT "Sgf29 binds histone H3K4me2/3 and is required for SAGA complex recruitment
RT and histone H3 acetylation.";
RL EMBO J. 30:2829-2842(2011).
RN [14]
RP FUNCTION.
RX PubMed=24307402; DOI=10.1093/jb/mvt108;
RA Kamata K., Goswami G., Kashio S., Urano T., Nakagawa R., Uchida H., Oki M.;
RT "The N-terminus and Tudor domains of Sgf29 are important for its
RT heterochromatin boundary formation function.";
RL J. Biochem. 155:159-171(2014).
CC -!- FUNCTION: Chromatin reader component of the transcription regulatory
CC histone acetylation (HAT) complexes SAGA and SLIK (PubMed:10026213,
CC PubMed:15647753, PubMed:21685874, PubMed:24307402). In the SAGA
CC complex, SGF29 specifically recognizes and binds methylated 'Lys-4' of
CC histone H3 (H3K4me), with a preference for trimethylated form (H3K4me3)
CC (PubMed:21685874). SGF29 is also required for heterochromatin boundary
CC formation function (PubMed:24307402). SAGA is involved in RNA
CC polymerase II-dependent transcriptional regulation of approximately 10%
CC of yeast genes At the promoters, SAGA is required for recruitment of
CC the basal transcription machinery (PubMed:10026213). It influences RNA
CC polymerase II transcriptional activity through different activities
CC such as TBP interaction (SPT3, SPT8 and SPT20) and promoter
CC selectivity, interaction with transcription activators (GCN5, ADA2,
CC ADA3 and TRA1), and chromatin modification through histone acetylation
CC (GCN5) and deubiquitination (UBP8) (PubMed:10026213). SAGA acetylates
CC nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac
CC and H3K23ac). SAGA interacts with DNA via upstream activating sequences
CC (UASs) (PubMed:10026213). SLIK is proposed to have partly overlapping
CC functions with SAGA (PubMed:15647753). It preferentially acetylates
CC methylated histone H3, at least after activation at the GAL1-10 locus
CC (PubMed:15647753). {ECO:0000269|PubMed:10026213,
CC ECO:0000269|PubMed:15647753, ECO:0000269|PubMed:21685874,
CC ECO:0000269|PubMed:24307402}.
CC -!- SUBUNIT: Component of the 1.8 MDa SAGA complex, which consists of at
CC least of TRA1, CHD1, SPT7, TAF5, ADA3, SGF73, SPT20/ADA5, SPT8, TAF12,
CC TAF6, HFI1/ADA1, UBP8, GCN5, ADA2, SPT3, SGF29, TAF10, TAF9, SGF11 and
CC SUS1. TAF5, TAF6, TAF9, TAF19, TAF12 and ADA1 seem to be present in 2
CC copies. SAGA is built of 5 distinct domains with specialized functions.
CC Domain I (containing TRA1) probably represents the activator
CC interaction surface. Domain II (containing TAF5 and TAF6, and probably
CC TAF9 and TAF10), domain III (containing GCN5, TAF10, SPT7, TAF5 and
CC ADA1, and probably ADA2, ADA3 and TAF12), and domain IV (containing
CC HFI1/ADA1 and TAF6, and probably TAF9) are believed to play primarily
CC an architectural role. Domain III also harbors the HAT activity. Domain
CC V (containing SPT3 and SPT20, and probably SPT8) represents the TBP-
CC interacting module, which may be associated transiently with SAGA.
CC Interacts with dimethylated and trimethylated 'Lys-4' of histone H3
CC (H3K4me2 and H3K4me3), with a preference for the trimethylated form
CC (H3K4me3). Component of the SLIK complex, which consists of at least
CC TRA1, CHD1, SPT7, TAF5, ADA3, SPT20, RTG2, TAF12, TAF6, HFI1, UBP8,
CC GCN5, ADA2, SPT3, SGF29, TAF10 and TAF9. {ECO:0000269|PubMed:12052880,
CC ECO:0000269|PubMed:15647753, ECO:0000269|PubMed:21685874}.
CC -!- INTERACTION:
CC P25554; Q12060: HFI1; NbExp=9; IntAct=EBI-21678, EBI-8287;
CC P25554; P32494: NGG1; NbExp=5; IntAct=EBI-21678, EBI-2192;
CC P25554; P68431: H3C12; Xeno; NbExp=11; IntAct=EBI-21678, EBI-79722;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- DOMAIN: The SGF29 C-terminal (also named tudor-like) domain mediates
CC binding to methylated 'Lys-4' of histone H3 (H3K4me).
CC {ECO:0000255|PROSITE-ProRule:PRU00851, ECO:0000269|PubMed:21685874}.
CC -!- MISCELLANEOUS: Present with 1750 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the SGF29 family. {ECO:0000255|PROSITE-
CC ProRule:PRU00851}.
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DR EMBL; X59720; CAA42349.1; -; Genomic_DNA.
DR EMBL; BK006937; DAA07471.1; -; Genomic_DNA.
DR PIR; S74287; S74287.
DR RefSeq; NP_009917.1; NM_001178659.1.
DR PDB; 3MP1; X-ray; 2.60 A; A=111-259.
DR PDB; 3MP6; X-ray; 1.48 A; A=111-259.
DR PDB; 3MP8; X-ray; 1.92 A; A=111-259.
DR PDBsum; 3MP1; -.
DR PDBsum; 3MP6; -.
DR PDBsum; 3MP8; -.
DR AlphaFoldDB; P25554; -.
DR SMR; P25554; -.
DR BioGRID; 30971; 570.
DR ComplexPortal; CPX-608; ADA complex.
DR ComplexPortal; CPX-656; SAGA complex.
DR ComplexPortal; CPX-675; SLIK (SAGA-like) complex.
DR DIP; DIP-4871N; -.
DR IntAct; P25554; 93.
DR MINT; P25554; -.
DR STRING; 4932.YCL010C; -.
DR iPTMnet; P25554; -.
DR MaxQB; P25554; -.
DR PaxDb; P25554; -.
DR PRIDE; P25554; -.
DR DNASU; 850347; -.
DR EnsemblFungi; YCL010C_mRNA; YCL010C; YCL010C.
DR GeneID; 850347; -.
DR KEGG; sce:YCL010C; -.
DR SGD; S000000516; SGF29.
DR VEuPathDB; FungiDB:YCL010C; -.
DR eggNOG; KOG3038; Eukaryota.
DR GeneTree; ENSGT00390000015229; -.
DR HOGENOM; CLU_023535_2_0_1; -.
DR InParanoid; P25554; -.
DR OMA; IYNANEV; -.
DR BioCyc; YEAST:G3O-29279-MON; -.
DR EvolutionaryTrace; P25554; -.
DR PRO; PR:P25554; -.
DR Proteomes; UP000002311; Chromosome III.
DR RNAct; P25554; protein.
DR GO; GO:0140671; C:ADA complex; IMP:SGD.
DR GO; GO:0005634; C:nucleus; IC:ComplexPortal.
DR GO; GO:0000124; C:SAGA complex; IDA:SGD.
DR GO; GO:0046695; C:SLIK (SAGA-like) complex; IPI:ComplexPortal.
DR GO; GO:0035064; F:methylated histone binding; IDA:SGD.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0016573; P:histone acetylation; IDA:ComplexPortal.
DR GO; GO:0016578; P:histone deubiquitination; IC:ComplexPortal.
DR GO; GO:0043966; P:histone H3 acetylation; IBA:GO_Central.
DR GO; GO:0044154; P:histone H3-K14 acetylation; IMP:SGD.
DR GO; GO:0043971; P:histone H3-K18 acetylation; IMP:SGD.
DR GO; GO:0043970; P:histone H3-K9 acetylation; IMP:SGD.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IMP:SGD.
DR GO; GO:0008104; P:protein localization; IMP:SGD.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IDA:ComplexPortal.
DR GO; GO:0072742; P:SAGA complex localization to transcription regulatory region; IMP:SGD.
DR CDD; cd04508; TUDOR; 1.
DR IDEAL; IID50141; -.
DR InterPro; IPR037802; SGF29.
DR InterPro; IPR010750; SGF29_tudor-like_dom.
DR InterPro; IPR002999; Tudor.
DR PANTHER; PTHR21539; PTHR21539; 1.
DR Pfam; PF07039; DUF1325; 1.
DR PROSITE; PS51518; SGF29_C; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chromatin regulator; Nucleus; Phosphoprotein;
KW Reference proteome; Transcription; Transcription regulation.
FT CHAIN 1..259
FT /note="SAGA-associated factor 29"
FT /id="PRO_0000202539"
FT DOMAIN 121..255
FT /note="SGF29 C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00851"
FT REGION 75..102
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 163..165
FT /note="Histone H3K4me3 N-terminus binding"
FT /evidence="ECO:0000269|PubMed:21685874"
FT REGION 207..210
FT /note="Histone H3K4me3 N-terminus binding"
FT /evidence="ECO:0000269|PubMed:21685874"
FT REGION 229..232
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000269|PubMed:21685874"
FT SITE 205
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000269|PubMed:21685874"
FT SITE 212
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000269|PubMed:21685874"
FT MOD_RES 139
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:15665377,
FT ECO:0007744|PubMed:17330950, ECO:0007744|PubMed:18407956,
FT ECO:0007744|PubMed:19779198"
FT MUTAGEN 163
FT /note="D->A: Reduces histone H3 acetylation."
FT /evidence="ECO:0000269|PubMed:21685874"
FT MUTAGEN 165
FT /note="E->A: Reduces histone H3 acetylation."
FT /evidence="ECO:0000269|PubMed:21685874"
FT MUTAGEN 205
FT /note="Y->A: Reduces histone H3 acetylation."
FT /evidence="ECO:0000269|PubMed:21685874"
FT MUTAGEN 210
FT /note="T->A: Reduces histone H3 acetylation."
FT /evidence="ECO:0000269|PubMed:21685874"
FT MUTAGEN 212
FT /note="Y->A: Reduces histone H3 acetylation."
FT /evidence="ECO:0000269|PubMed:21685874"
FT MUTAGEN 229
FT /note="F->A: Reduces histone H3 acetylation."
FT /evidence="ECO:0000269|PubMed:21685874"
FT STRAND 105..107
FT /evidence="ECO:0007829|PDB:3MP1"
FT STRAND 118..120
FT /evidence="ECO:0007829|PDB:3MP6"
FT STRAND 130..133
FT /evidence="ECO:0007829|PDB:3MP6"
FT TURN 140..142
FT /evidence="ECO:0007829|PDB:3MP8"
FT STRAND 144..153
FT /evidence="ECO:0007829|PDB:3MP6"
FT TURN 154..157
FT /evidence="ECO:0007829|PDB:3MP6"
FT STRAND 158..163
FT /evidence="ECO:0007829|PDB:3MP6"
FT STRAND 174..178
FT /evidence="ECO:0007829|PDB:3MP6"
FT HELIX 180..182
FT /evidence="ECO:0007829|PDB:3MP6"
FT STRAND 183..186
FT /evidence="ECO:0007829|PDB:3MP6"
FT STRAND 200..204
FT /evidence="ECO:0007829|PDB:3MP6"
FT STRAND 209..219
FT /evidence="ECO:0007829|PDB:3MP6"
FT STRAND 225..229
FT /evidence="ECO:0007829|PDB:3MP6"
FT STRAND 232..234
FT /evidence="ECO:0007829|PDB:3MP8"
FT STRAND 239..241
FT /evidence="ECO:0007829|PDB:3MP6"
FT HELIX 243..245
FT /evidence="ECO:0007829|PDB:3MP6"
FT STRAND 246..248
FT /evidence="ECO:0007829|PDB:3MP6"
FT HELIX 250..253
FT /evidence="ECO:0007829|PDB:3MP6"
SQ 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
