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SAGA-associated factor 29 (Coiled-coil domain-containing protein 101) (SAGA complex-associated factor 29)

 SGF29_HUMAN             Reviewed;         293 AA.
Q96ES7; Q96MF5;
06-FEB-2007, integrated into UniProtKB/Swiss-Prot.
01-DEC-2001, sequence version 1.
25-OCT-2017, entry version 121.
RecName: Full=SAGA-associated factor 29 {ECO:0000305};
AltName: Full=Coiled-coil domain-containing protein 101;
AltName: Full=SAGA complex-associated factor 29 {ECO:0000312|HGNC:HGNC:25156};
Name=SGF29 {ECO:0000312|HGNC:HGNC:25156};
Synonyms=CCDC101 {ECO:0000312|HGNC:HGNC:25156};
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
TISSUE=Skeletal muscle;
PubMed=14702039; DOI=10.1038/ng1285;
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A.,
Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M.,
Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y.,
Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M.,
Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K.,
Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S.,
Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J.,
Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y.,
Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N.,
Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S.,
Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y.,
Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T.,
Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y.,
Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S.,
Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T.,
Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M.,
Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T.,
Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K.,
Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R.,
Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.;
"Complete sequencing and characterization of 21,243 full-length human
cDNAs.";
Nat. Genet. 36:40-45(2004).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
TISSUE=Ovary;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[3]
FUNCTION, AND IDENTIFICATION IN ATAC COMPLEX.
PubMed=19103755; DOI=10.1128/MCB.01599-08;
Guelman S., Kozuka K., Mao Y., Pham V., Solloway M.J., Wang J., Wu J.,
Lill J.R., Zha J.;
"The double-histone-acetyltransferase complex ATAC is essential for
mammalian development.";
Mol. Cell. Biol. 29:1176-1188(2009).
[4]
ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-288, AND IDENTIFICATION BY
MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19608861; DOI=10.1126/science.1175371;
Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M.,
Walther T.C., Olsen J.V., Mann M.;
"Lysine acetylation targets protein complexes and co-regulates major
cellular functions.";
Science 325:834-840(2009).
[5]
FUNCTION, METHYLATED HISTONE-BINDING, IDENTIFICATION IN A SAGA-TYPE
COMPLEX, AND MUTAGENESIS OF TRP-175; GLU-179; PRO-214; GLN-232;
TYR-238; TYR-245; PRO-256; PHE-264 AND ARG-282.
PubMed=20850016; DOI=10.1016/j.cell.2010.08.020;
Vermeulen M., Eberl H.C., Matarese F., Marks H., Denissov S.,
Butter F., Lee K.K., Olsen J.V., Hyman A.A., Stunnenberg H.G.,
Mann M.;
"Quantitative interaction proteomics and genome-wide profiling of
epigenetic histone marks and their readers.";
Cell 142:967-980(2010).
[6]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=21269460; DOI=10.1186/1752-0509-5-17;
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P.,
Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.;
"Initial characterization of the human central proteome.";
BMC Syst. Biol. 5:17-17(2011).
[7]
FUNCTION.
PubMed=23894581; DOI=10.1371/journal.pone.0070035;
Schram A.W., Baas R., Jansen P.W., Riss A., Tora L., Vermeulen M.,
Timmers H.T.;
"A dual role for SAGA-associated factor 29 (SGF29) in ER stress
survival by coordination of both histone H3 acetylation and histone H3
lysine-4 trimethylation.";
PLoS ONE 8:E70035-E70035(2013).
[8]
DOMAIN, FUNCTION, AND MUTAGENESIS OF TYR-238; TYR-245 AND ASP-266.
PubMed=26421618; DOI=10.1371/journal.pone.0139205;
Pieters B.J., Meulenbroeks E., Belle R., Mecinovic J.;
"The role of electrostatic interactions in binding of histone
H3K4me2/3 to the Sgf29 tandem Tudor domain.";
PLoS ONE 10:E0139205-E0139205(2015).
[9]
X-RAY CRYSTALLOGRAPHY (1.26 ANGSTROMS) OF 115-293 IN COMPLEX WITH
H3K4ME2 PEPTIDE, FUNCTION, INTERACTION WITH H3K4ME2 AND H3K4ME3,
MUTAGENESIS OF ASP-194; ASP-196; TYR-238; GLN-240; THR-242; TYR-245;
PHE-264 AND ASP-266, AND DOMAIN.
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).
[10] {ECO:0000244|PDB:5C0M}
X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF 115-293 IN COMPLEX WITH
H3K4ME3 PEPTIDE, DOMAIN, AND FUNCTION.
PubMed=26578293; DOI=10.1038/ncom$ms9911;
Kamps J.J., Huang J., Poater J., Xu C., Pieters B.J., Dong A., Min J.,
Sherman W., Beuming T., Matthias Bickelhaupt F., Li H., Mecinovic J.;
"Chemical basis for the recognition of trimethyllysine by epigenetic
reader proteins.";
Nat. Commun. 6:8911-8911(2015).
-!- FUNCTION: Chromatin reader component of some histone
acetyltransferase (HAT) SAGA-type complexes like the TFTC-HAT,
ATAC or STAGA complexes (PubMed:19103755, PubMed:20850016,
PubMed:26421618, PubMed:21685874, PubMed:26578293). SGF29
specifically recognizes and binds methylated 'Lys-4' of histone H3
(H3K4me), with a preference for trimethylated form (H3K4me3)
(PubMed:20850016, PubMed:26421618, PubMed:21685874,
PubMed:26578293). In the SAGA-type complexes, SGF29 is required to
recruit complexes to H3K4me (PubMed:20850016). Involved in the
response to endoplasmic reticulum (ER) stress by recruiting the
SAGA complex to H3K4me, thereby promoting histone H3 acetylation
and cell survival (PubMed:23894581). {ECO:0000269|PubMed:19103755,
ECO:0000269|PubMed:20850016, ECO:0000269|PubMed:21685874,
ECO:0000269|PubMed:23894581, ECO:0000269|PubMed:26421618,
ECO:0000269|PubMed:26578293}.
-!- SUBUNIT: Interacts with dimethylated and trimethylated 'Lys-4' of
histone H3 (H3K4me2 and H3K4me3), with a preference for the
trimethylated form (H3K4me3) (PubMed:21685874, PubMed:26578293).
Component of some SAGA-type complexes (PubMed:20850016). Component
of the ADA2A-containing complex (ATAC), composed of KAT14, KAT2A,
TADA2L, TADA3L, ZZ3, MBIP, WDR5, YEATS2, CCDC101 and DR1
(PubMed:19103755). Interacts with TADA3L, GCN5L2, SUPT3H and MYC
(By similarity). {ECO:0000250|UniProtKB:P0C606,
ECO:0000269|PubMed:19103755, ECO:0000269|PubMed:20850016,
ECO:0000269|PubMed:21685874, ECO:0000269|PubMed:26578293}.
-!- INTERACTION:
Q14457:BECN1; NbExp=4; IntAct=EBI-743117, EBI-949378;
Q68D86:CCDC102B; NbExp=3; IntAct=EBI-743117, EBI-10171570;
Q8NHS4:CLHC1; NbExp=3; IntAct=EBI-743117, EBI-10203156;
P68431:HIST1H3D; NbExp=25; IntAct=EBI-743117, EBI-79722;
A1A4E9:KRT13; NbExp=3; IntAct=EBI-743117, EBI-10171552;
P19012:KRT15; NbExp=6; IntAct=EBI-743117, EBI-739566;
Q14525:KRT33B; NbExp=4; IntAct=EBI-743117, EBI-1049638;
Q8TBB1:LNX1; NbExp=3; IntAct=EBI-743117, EBI-739832;
Q9NPJ6:MED4; NbExp=3; IntAct=EBI-743117, EBI-394607;
O14777:NDC80; NbExp=6; IntAct=EBI-743117, EBI-715849;
Q6NUQ1:RINT1; NbExp=5; IntAct=EBI-743117, EBI-726876;
O75528:TADA3; NbExp=9; IntAct=EBI-743117, EBI-473249;
P15884:TCF4; NbExp=4; IntAct=EBI-743117, EBI-533224;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:P0C606}.
-!- DOMAIN: The SGF29 C-terminal (also named tudor-like) domain
mediates binding to methylated 'Lys-4' of histone H3 (H3K4me),
with a preference for trimethylated form (H3K4me3).
{ECO:0000255|PROSITE-ProRule:PRU00851,
ECO:0000269|PubMed:21685874, ECO:0000269|PubMed:26421618,
ECO:0000269|PubMed:26578293}.
-!- SIMILARITY: Belongs to the SGF29 family. {ECO:0000255|PROSITE-
ProRule:PRU00851}.
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EMBL; AK057008; BAB71340.1; -; mRNA.
EMBL; BC011981; AAH11981.1; -; mRNA.
CCDS; CCDS10635.1; -.
RefSeq; NP_612423.1; NM_138414.2.
UniGene; Hs.655476; -.
PDB; 3LX7; X-ray; 1.78 A; A=138-293.
PDB; 3ME9; X-ray; 1.37 A; A/B=115-293.
PDB; 3MEA; X-ray; 1.26 A; A=129-291.
PDB; 3MET; X-ray; 2.00 A; A/B=115-293.
PDB; 3MEU; X-ray; 1.28 A; A/B=115-293.
PDB; 3MEV; X-ray; 1.83 A; A/B=115-293.
PDB; 3MEW; X-ray; 1.92 A; A=129-287.
PDB; 5C0M; X-ray; 1.60 A; A/B=115-293.
PDBsum; 3LX7; -.
PDBsum; 3ME9; -.
PDBsum; 3MEA; -.
PDBsum; 3MET; -.
PDBsum; 3MEU; -.
PDBsum; 3MEV; -.
PDBsum; 3MEW; -.
PDBsum; 5C0M; -.
ProteinModelPortal; Q96ES7; -.
SMR; Q96ES7; -.
BioGrid; 125213; 92.
CORUM; Q96ES7; -.
IntAct; Q96ES7; 50.
MINT; MINT-3976256; -.
STRING; 9606.ENSP00000316114; -.
iPTMnet; Q96ES7; -.
PhosphoSitePlus; Q96ES7; -.
BioMuta; CCDC101; -.
DMDM; 74731608; -.
EPD; Q96ES7; -.
MaxQB; Q96ES7; -.
PaxDb; Q96ES7; -.
PeptideAtlas; Q96ES7; -.
PRIDE; Q96ES7; -.
Ensembl; ENST00000317058; ENSP00000316114; ENSG00000176476.
GeneID; 112869; -.
KEGG; hsa:112869; -.
UCSC; uc002dqf.4; human.
CTD; 112869; -.
DisGeNET; 112869; -.
EuPathDB; HostDB:ENSG00000176476.8; -.
GeneCards; SGF29; -.
HGNC; HGNC:25156; SGF29.
HPA; HPA052590; -.
HPA; HPA053608; -.
MIM; 613374; gene.
neXtProt; NX_Q96ES7; -.
OpenTargets; ENSG00000176476; -.
PharmGKB; PA144596468; -.
eggNOG; KOG3038; Eukaryota.
eggNOG; ENOG410XPFD; LUCA.
GeneTree; ENSGT00390000015229; -.
HOGENOM; HOG000006769; -.
HOVERGEN; HBG059575; -.
InParanoid; Q96ES7; -.
KO; K11364; -.
OMA; TCFYKAV; -.
OrthoDB; EOG091G0G88; -.
PhylomeDB; Q96ES7; -.
TreeFam; TF314958; -.
Reactome; R-HSA-3214847; HATs acetylate histones.
EvolutionaryTrace; Q96ES7; -.
GenomeRNAi; 112869; -.
PRO; PR:Q96ES7; -.
Proteomes; UP000005640; Chromosome 16.
Bgee; ENSG00000176476; -.
CleanEx; HS_CCDC101; -.
ExpressionAtlas; Q96ES7; baseline and differential.
Genevisible; Q96ES7; HS.
GO; GO:0005671; C:Ada2/Gcn5/Ada3 transcription activator complex; IDA:BHF-UCL.
GO; GO:0070461; C:SAGA-type complex; IDA:UniProtKB.
GO; GO:0035064; F:methylated histone binding; IDA:UniProtKB.
GO; GO:0071169; P:establishment of protein localization to chromatin; TAS:UniProtKB.
GO; GO:0016573; P:histone acetylation; IDA:UniProtKB.
GO; GO:0043966; P:histone H3 acetylation; IDA:BHF-UCL.
GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:UniProtKB-KW.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
InterPro; IPR010750; SGF29_tudor-like_dom.
Pfam; PF07039; DUF1325; 1.
PROSITE; PS51518; SGF29_C; 1.
1: Evidence at protein level;
3D-structure; Acetylation; Chromatin regulator; Coiled coil;
Complete proteome; Nucleus; Reference proteome; Transcription;
Transcription regulation.
CHAIN 1 293 SAGA-associated factor 29.
/FTId=PRO_0000274268.
DOMAIN 152 293 SGF29 C-terminal. {ECO:0000255|PROSITE-
ProRule:PRU00851}.
REGION 194 196 Histone H3K4me3 N-terminus binding.
{ECO:0000269|PubMed:21685874,
ECO:0000269|PubMed:26578293}.
REGION 240 243 Histone H3K4me3 N-terminus binding.
{ECO:0000269|PubMed:21685874,
ECO:0000269|PubMed:26578293}.
REGION 264 266 Histone H3K4me3 binding.
{ECO:0000269|PubMed:21685874}.
COILED 3 88 {ECO:0000255}.
BINDING 238 238 Histone H3K4me3.
{ECO:0000269|PubMed:21685874}.
BINDING 245 245 Histone H3K4me3.
{ECO:0000269|PubMed:21685874,
ECO:0000269|PubMed:26578293}.
MOD_RES 288 288 N6-acetyllysine.
{ECO:0000244|PubMed:19608861}.
MUTAGEN 175 175 W->A: Does not strongly affect binding to
H3K4me. {ECO:0000269|PubMed:20850016}.
MUTAGEN 179 179 E->A: Does not strongly affect binding to
H3K4me. {ECO:0000269|PubMed:20850016}.
MUTAGEN 194 194 D->A,R: Abolishes H3K4me3 binding.
{ECO:0000269|PubMed:21685874}.
MUTAGEN 196 196 D->R: Abolishes H3K4me3 binding.
{ECO:0000269|PubMed:21685874}.
MUTAGEN 214 214 P->A: Does not strongly affect binding to
H3K4me. {ECO:0000269|PubMed:20850016}.
MUTAGEN 232 232 Q->A: Does not strongly affect binding to
H3K4me. {ECO:0000269|PubMed:20850016}.
MUTAGEN 238 238 Y->A: Strongly reduced H3K4me3 binding.
{ECO:0000269|PubMed:20850016,
ECO:0000269|PubMed:21685874}.
MUTAGEN 238 238 Y->F: Does not affect binding to H3K4me3.
{ECO:0000269|PubMed:26421618}.
MUTAGEN 240 240 Q->A: Slightly reduced H3K4me3 binding.
{ECO:0000269|PubMed:21685874}.
MUTAGEN 242 242 T->A: Almost abolished H3K4me3 binding.
{ECO:0000269|PubMed:21685874}.
MUTAGEN 245 245 Y->A: Abolishes H3K4me3 binding.
{ECO:0000269|PubMed:20850016,
ECO:0000269|PubMed:21685874}.
MUTAGEN 245 245 Y->F: Reduced H3K4me3 binding.
{ECO:0000269|PubMed:26421618}.
MUTAGEN 256 256 P->A: Does not strongly affect binding to
H3K4me. {ECO:0000269|PubMed:20850016}.
MUTAGEN 264 264 F->A: Strongly reduced binding to
H3K4me3. {ECO:0000269|PubMed:20850016,
ECO:0000269|PubMed:21685874}.
MUTAGEN 266 266 D->A,F,Y,W: Strongly reduced binding to
H3K4me3. {ECO:0000269|PubMed:21685874,
ECO:0000269|PubMed:26421618}.
MUTAGEN 266 266 D->E: Does not affect binding to H3K4me3.
{ECO:0000269|PubMed:26421618}.
MUTAGEN 266 266 D->N: Slightly reduced binding to
H3K4me3. {ECO:0000269|PubMed:26421618}.
MUTAGEN 282 282 R->A: Does not strongly affect binding to
H3K4me. {ECO:0000269|PubMed:20850016}.
CONFLICT 249 249 I -> N (in Ref. 1; BAB71340).
{ECO:0000305}.
HELIX 115 129 {ECO:0000244|PDB:3MEU}.
STRAND 161 167 {ECO:0000244|PDB:3MEA}.
STRAND 173 184 {ECO:0000244|PDB:3MEA}.
TURN 185 188 {ECO:0000244|PDB:3MEA}.
STRAND 189 194 {ECO:0000244|PDB:3MEA}.
STRAND 201 206 {ECO:0000244|PDB:3MEA}.
HELIX 207 209 {ECO:0000244|PDB:3MEA}.
STRAND 210 212 {ECO:0000244|PDB:3MEA}.
STRAND 215 217 {ECO:0000244|PDB:3MEA}.
TURN 220 222 {ECO:0000244|PDB:3MEA}.
HELIX 224 226 {ECO:0000244|PDB:3MEA}.
STRAND 233 237 {ECO:0000244|PDB:3MEA}.
STRAND 241 251 {ECO:0000244|PDB:3MEA}.
STRAND 260 265 {ECO:0000244|PDB:3MEA}.
STRAND 277 279 {ECO:0000244|PDB:3MEA}.
HELIX 281 283 {ECO:0000244|PDB:3MEA}.
STRAND 284 286 {ECO:0000244|PDB:3MEA}.
SEQUENCE 293 AA; 33238 MW; A1B4A8D9B0044CC7 CRC64;
MALVSADSRI AELLTELHQL IKQTQEERSR SEHNLVNIQK THERMQTENK ISPYYRTKLR
GLYTTAKADA EAECNILRKA LDKIAEIKSL LEERRIAAKI AGLYNDSEPP RKTMRRGVLM
TLLQQSAMTL PLWIGKPGDK PPPLCGAIPA SGDYVARPGD KVAARVKAVD GDEQWILAEV
VSYSHATNKY EVDDIDEEGK ERHTLSRRRV IPLPQWKANP ETDPEALFQK EQLVLALYPQ
TTCFYRALIH APPQRPQDDY SVLFEDTSYA DGYSPPLNVA QRYVVACKEP KKK


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