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Histone-lysine N-methyltransferase SETDB1 (EC 2.1.1.43) (ERG-associated protein with SET domain) (ESET) (Histone H3-K9 methyltransferase 4) (H3-K9-HMTase 4) (Lysine N-methyltransferase 1E) (SET domain bifurcated 1)

 SETB1_HUMAN             Reviewed;        1291 AA.
Q15047; A6NEW2; Q5SZD8; Q5SZD9; Q5SZE0; Q5SZE7; Q96GM9;
15-NOV-2002, integrated into UniProtKB/Swiss-Prot.
01-NOV-1996, sequence version 1.
12-SEP-2018, entry version 200.
RecName: Full=Histone-lysine N-methyltransferase SETDB1;
EC=2.1.1.43;
AltName: Full=ERG-associated protein with SET domain;
Short=ESET;
AltName: Full=Histone H3-K9 methyltransferase 4;
Short=H3-K9-HMTase 4;
AltName: Full=Lysine N-methyltransferase 1E;
AltName: Full=SET domain bifurcated 1;
Name=SETDB1; Synonyms=KIAA0067, KMT1E;
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] (ISOFORM 1).
TISSUE=Bone marrow;
PubMed=7584044; DOI=10.1093/dnares/1.5.223;
Nomura N., Nagase T., Miyajima N., Sazuka T., Tanaka A., Sato S.,
Seki N., Kawarabayasi Y., Ishikawa K., Tabata S.;
"Prediction of the coding sequences of unidentified human genes. II.
The coding sequences of 40 new genes (KIAA0041-KIAA0080) deduced by
analysis of cDNA clones from human cell line KG-1.";
DNA Res. 1:223-229(1994).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=16710414; DOI=10.1038/nature04727;
Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D.,
Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A.,
Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F.,
McDonald L., Evans R., Phillips K., Atkinson A., Cooper R., Jones C.,
Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P.,
Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K.,
Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G.,
Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D.,
Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G.,
Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J.,
Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H.,
Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L.,
Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J.,
Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R.,
Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D.,
Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G.,
Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M.,
Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J.,
Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M.,
Loveland J., Lovell J., Lush M.J., Lyne R., Martin S.,
Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S.,
Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N.,
Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V.,
Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J.,
Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E.,
Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C.,
Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z.,
Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E.,
Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A.,
Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R.,
Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V.,
Beck S., Rogers J., Bentley D.R.;
"The DNA sequence and biological annotation of human chromosome 1.";
Nature 441:315-321(2006).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L.,
Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R.,
Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V.,
Hannenhalli S., Turner R., Yooseph S., Lu F., Nusskern D.R.,
Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H.,
Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G.,
Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W.,
Venter J.C.;
Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases.
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1; 2 AND 3), AND
VARIANT SER-506.
TISSUE=Muscle, and Uterus;
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).
[5]
CHARACTERIZATION, MUTAGENESIS OF 729-CYS--CYS-731; HIS-1224; CYS-1226
AND CYS-1279, AND INTERACTION WITH TRIM28.
PubMed=11959841; DOI=10.1101/gad.973302;
Schultz D.C., Ayyanathan K., Negorev D., Maul G.G., Rauscher F.J. III;
"SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific
methyltransferase that contributes to HP1-mediated silencing of
euchromatic genes by KRAB zinc-finger proteins.";
Genes Dev. 16:919-932(2002).
[6]
FUNCTION.
PubMed=12869583; DOI=10.1101/gad.1102803;
Ayyanathan K., Lechner M.S., Bell P., Maul G.G., Schultz D.C.,
Yamada Y., Tanaka K., Torigoe K., Rauscher F.J. III;
"Regulated recruitment of HP1 to a euchromatic gene induces
mitotically heritable, epigenetic gene silencing: a mammalian cell
culture model of gene variegation.";
Genes Dev. 17:1855-1869(2003).
[7]
IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, AND INTERACTION WITH
ATF7IP.
PubMed=14536086; DOI=10.1016/j.molcel.2003.08.007;
Wang H., An W., Cao R., Xia L., Erdjument-Bromage H., Chatton B.,
Tempst P., Roeder R.G., Zhang Y.;
"mAM facilitates conversion by ESET of dimethyl to trimethyl lysine 9
of histone H3 to cause transcriptional repression.";
Mol. Cell 12:475-487(2003).
[8]
FUNCTION, AND INTERACTION WITH MBD1 AND CHAF1A.
PubMed=15327775; DOI=10.1016/j.molcel.2004.06.043;
Sarraf S.A., Stancheva I.;
"Methyl-CpG binding protein MBD1 couples histone H3 methylation at
lysine 9 by SETDB1 to DNA replication and chromatin assembly.";
Mol. Cell 15:595-605(2004).
[9]
INTERACTION WITH CBX1 AND CBX5.
PubMed=15899859; DOI=10.1128/MCB.25.11.4552-4564.2005;
Verschure P.J., van der Kraan I., de Leeuw W., van der Vlag J.,
Carpenter A.E., Belmont A.S., van Driel R.;
"In vivo HP1 targeting causes large-scale chromatin condensation and
enhanced histone lysine methylation.";
Mol. Cell. Biol. 25:4552-4564(2005).
[10]
INTERACTION WITH MBD1.
PubMed=17066076; DOI=10.1038/sj.emboj.7601404;
Lyst M.J., Nan X., Stancheva I.;
"Regulation of MBD1-mediated transcriptional repression by SUMO and
PIAS proteins.";
EMBO J. 25:5317-5328(2006).
[11]
INTERACTION WITH ATF7IP AND ATF7IP2.
PubMed=15691849; DOI=10.1074/jbc.M413654200;
Ichimura T., Watanabe S., Sakamoto Y., Aoto T., Fujita N., Nakao M.;
"Transcriptional repression and heterochromatin formation by MBD1 and
MCAF/AM family proteins.";
J. Biol. Chem. 280:13928-13935(2005).
[12]
INTERACTION WITH DNMT3A AND DNMT3B.
PubMed=16682412; DOI=10.1074/jbc.M513249200;
Li H., Rauch T., Chen Z.-X., Szabo P.E., Riggs A.D., Pfeifer G.P.;
"The histone methyltransferase SETDB1 and the DNA methyltransferase
DNMT3A interact directly and localize to promoters silenced in cancer
cells.";
J. Biol. Chem. 281:19489-19500(2006).
[13]
INTERACTION WITH SUMO2.
PubMed=16567619; DOI=10.1073/pnas.0601066103;
Rosendorff A., Sakakibara S., Lu S., Kieff E., Xuan Y., DiBacco A.,
Shi Y., Shi Y., Gill G.;
"NXP-2 association with SUMO-2 depends on lysines required for
transcriptional repression.";
Proc. Natl. Acad. Sci. U.S.A. 103:5308-5313(2006).
[14]
EXPRESSION IN HUNTINGTON DISEASE.
PubMed=17142323; DOI=10.1073/pnas.0606373103;
Ryu H., Lee J., Hagerty S.W., Soh B.Y., McAlpin S.E., Cormier K.A.,
Smith K.M., Ferrante R.J.;
"ESET/SETDB1 gene expression and histone H3 (K9) trimethylation in
Huntington's disease.";
Proc. Natl. Acad. Sci. U.S.A. 103:19176-19181(2006).
[15]
FUNCTION, INTERACTION WITH CHD7; NLK1 AND PPARG, PHOSPHORYLATION AT
THR-976, AND MUTAGENESIS OF THR-976.
PubMed=17952062; DOI=10.1038/ncb1647;
Takada I., Mihara M., Suzawa M., Ohtake F., Kobayashi S., Igarashi M.,
Youn M.Y., Takeyama K., Nakamura T., Mezaki Y., Takezawa S.,
Yogiashi Y., Kitagawa H., Yamada G., Takada S., Minami Y., Shibuya H.,
Matsumoto K., Kato S.;
"A histone lysine methyltransferase activated by non-canonical Wnt
signalling suppresses PPAR-gamma transactivation.";
Nat. Cell Biol. 9:1273-1285(2007).
[16]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1066, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Cervix carcinoma;
PubMed=18220336; DOI=10.1021/pr0705441;
Cantin G.T., Yi W., Lu B., Park S.K., Xu T., Lee J.-D.,
Yates J.R. III;
"Combining protein-based IMAC, peptide-based IMAC, and MudPIT for
efficient phosphoproteomic analysis.";
J. Proteome Res. 7:1346-1351(2008).
[17]
IDENTIFICATION IN A COMPLEX WITH REST; CDYL; WIZ; EHMT1 AND EHMT2.
PubMed=19061646; DOI=10.1016/j.molcel.2008.10.025;
Mulligan P., Westbrook T.F., Ottinger M., Pavlova N., Chang B.,
Macia E., Shi Y.J., Barretina J., Liu J., Howley P.M., Elledge S.J.,
Shi Y.;
"CDYL bridges REST and histone methyltransferases for gene repression
and suppression of cellular transformation.";
Mol. Cell 32:718-726(2008).
[18]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1066, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Cervix carcinoma;
PubMed=18669648; DOI=10.1073/pnas.0805139105;
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
Elledge S.J., Gygi S.P.;
"A quantitative atlas of mitotic phosphorylation.";
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
[19]
INTERACTION WITH MPHOSPH8.
PubMed=20871592; DOI=10.1038/emboj.2010.239;
Kokura K., Sun L., Bedford M.T., Fang J.;
"Methyl-H3K9-binding protein MPP8 mediates E-cadherin gene silencing
and promotes tumour cell motility and invasion.";
EMBO J. 29:3673-3687(2010).
[20]
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).
[21]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1066, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=21406692; DOI=10.1126/scisignal.2001570;
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J.,
Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V.,
Blagoev B.;
"System-wide temporal characterization of the proteome and
phosphoproteome of human embryonic stem cell differentiation.";
Sci. Signal. 4:RS3-RS3(2011).
[22]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1025 AND SER-1066, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Cervix carcinoma, and Erythroleukemia;
PubMed=23186163; DOI=10.1021/pr300630k;
Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J.,
Mohammed S.;
"Toward a comprehensive characterization of a human cancer cell
phosphoproteome.";
J. Proteome Res. 12:260-271(2013).
[23]
FUNCTION, POSSIBLE IDENTIFICATION IN A COREPRESSOR COMPLEX, AND
CHROMATIN-BINDING.
PubMed=24623306; DOI=10.7554/eLife.02313;
Serra R.W., Fang M., Park S.M., Hutchinson L., Green M.R.;
"A KRAS-directed transcriptional silencing pathway that mediates the
CpG island methylator phenotype.";
Elife 3:E02313-E02313(2014).
[24]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Liver;
PubMed=24275569; DOI=10.1016/j.jprot.2013.11.014;
Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D.,
Wang L., Ye M., Zou H.;
"An enzyme assisted RP-RPLC approach for in-depth analysis of human
liver phosphoproteome.";
J. Proteomics 96:253-262(2014).
[25]
METHYLATION [LARGE SCALE ANALYSIS] AT LYS-1170 AND LYS-1178, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Colon carcinoma;
PubMed=24129315; DOI=10.1074/mcp.O113.027870;
Guo A., Gu H., Zhou J., Mulhern D., Wang Y., Lee K.A., Yang V.,
Aguiar M., Kornhauser J., Jia X., Ren J., Beausoleil S.A., Silva J.C.,
Vemulapalli V., Bedford M.T., Comb M.J.;
"Immunoaffinity enrichment and mass spectrometry analysis of protein
methylation.";
Mol. Cell. Proteomics 13:372-387(2014).
[26]
SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-1032 AND LYS-1069, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=25218447; DOI=10.1038/nsmb.2890;
Hendriks I.A., D'Souza R.C., Yang B., Verlaan-de Vries M., Mann M.,
Vertegaal A.C.;
"Uncovering global SUMOylation signaling networks in a site-specific
manner.";
Nat. Struct. Mol. Biol. 21:927-936(2014).
[27]
SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-1032, AND IDENTIFICATION BY
MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=25114211; DOI=10.1073/pnas.1413825111;
Impens F., Radoshevich L., Cossart P., Ribet D.;
"Mapping of SUMO sites and analysis of SUMOylation changes induced by
external stimuli.";
Proc. Natl. Acad. Sci. U.S.A. 111:12432-12437(2014).
[28]
SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-1032 AND LYS-1069, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=25772364; DOI=10.1016/j.celrep.2015.02.033;
Hendriks I.A., Treffers L.W., Verlaan-de Vries M., Olsen J.V.,
Vertegaal A.C.;
"SUMO-2 orchestrates chromatin modifiers in response to DNA damage.";
Cell Rep. 10:1778-1791(2015).
[29]
SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-1032 AND LYS-1069, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=25755297; DOI=10.1074/mcp.O114.044792;
Xiao Z., Chang J.G., Hendriks I.A., Sigurdsson J.O., Olsen J.V.,
Vertegaal A.C.;
"System-wide analysis of SUMOylation dynamics in response to
replication stress reveals novel small ubiquitin-like modified target
proteins and acceptor lysines relevant for genome stability.";
Mol. Cell. Proteomics 14:1419-1434(2015).
[30]
FUNCTION, INTERACTION WITH ATRX, AND FORMATION OF A COMPLEX WITH ATRX;
TRIM28 AND ZNF274.
PubMed=27029610; DOI=10.1080/15592294.2016.1169351;
Valle-Garcia D., Qadeer Z.A., McHugh D.S., Ghiraldini F.G.,
Chowdhury A.H., Hasson D., Dyer M.A., Recillas-Targa F., Bernstein E.;
"ATRX binds to atypical chromatin domains at the 3' exons of zinc
finger genes to preserve H3K9me3 enrichment.";
Epigenetics 11:398-414(2016).
[31]
SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-182; LYS-1032; LYS-1038;
LYS-1069 AND LYS-1149, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE
SCALE ANALYSIS].
PubMed=28112733; DOI=10.1038/nsmb.3366;
Hendriks I.A., Lyon D., Young C., Jensen L.J., Vertegaal A.C.,
Nielsen M.L.;
"Site-specific mapping of the human SUMO proteome reveals co-
modification with phosphorylation.";
Nat. Struct. Mol. Biol. 24:325-336(2017).
[32]
X-RAY CRYSTALLOGRAPHY (1.77 ANGSTROMS) OF 196-402.
Structural genomics consortium (SGC);
"The crystal structure of Tudor domain of human histone-lysine N-
methyltransferase SETDB1.";
Submitted (FEB-2009) to the PDB data bank.
-!- FUNCTION: Histone methyltransferase that specifically
trimethylates 'Lys-9' of histone H3. H3 'Lys-9' trimethylation
represents a specific tag for epigenetic transcriptional
repression by recruiting HP1 (CBX1, CBX3 and/or CBX5) proteins to
methylated histones. Mainly functions in euchromatin regions,
thereby playing a central role in the silencing of euchromatic
genes. H3 'Lys-9' trimethylation is coordinated with DNA
methylation. Probably forms a complex with MBD1 and ATF7IP that
represses transcription and couples DNA methylation and histone
'Lys-9' trimethylation. Its activity is dependent on MBD1 and is
heritably maintained through DNA replication by being recruited by
CAF-1. SETDB1 is targeted to histone H3 by TRIM28/TIF1B, a factor
recruited by KRAB zinc-finger proteins. Probably forms a
corepressor complex required for activated KRAS-mediated promoter
hypermethylation and transcriptional silencing of tumor suppressor
genes (TSGs) or other tumor-related genes in colorectal cancer
(CRC) cells (PubMed:24623306). Also required to maintain a
transcriptionally repressive state of genes in undifferentiated
embryonic stem cells (ESCs) (PubMed:24623306). Associates at
promoter regions of tumor suppressor genes (TSGs) leading to their
gene silencing (PubMed:24623306). The SETDB1-TRIM28-ZNF274 complex
may play a role in recruiting ATRX to the 3'-exons of zinc-finger
coding genes with atypical chromatin signatures to establish or
maintain/protect H3K9me3 at these transcriptionally active regions
(PubMed:27029610). {ECO:0000269|PubMed:12869583,
ECO:0000269|PubMed:14536086, ECO:0000269|PubMed:15327775,
ECO:0000269|PubMed:17952062, ECO:0000269|PubMed:24623306,
ECO:0000269|PubMed:27029610}.
-!- CATALYTIC ACTIVITY: S-adenosyl-L-methionine + L-lysine-[histone] =
S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
{ECO:0000255|PROSITE-ProRule:PRU00906}.
-!- SUBUNIT: Part of a complex containing at least CDYL, REST, WIZ,
SETB1, EHMT1 and EHMT2 (PubMed:19061646). During DNA replication,
it is recruited by SETDB1 to form a S phase-specific complex that
facilitates methylation of H3 'Lys-9' during replication-coupled
chromatin assembly and is at least composed of the CAF-1 subunit
CHAF1A, MBD1 and SETDB1 (PubMed:15327775). Probably part of a
corepressor complex containing ZNF304, TRIM28, SETDB1 and DNMT1
(PubMed:24623306). Interacts with TRIM28/TIF1B (PubMed:11959841).
Interacts with ATF7IP and ATF7IP2; the interaction with ATF7IP is
required to stimulate histone methyltransferase activity and
facilitate the conversion of dimethylated to trimethylated H3
'Lys-9' (PubMed:14536086, PubMed:15691849). Interacts with MBD1;
interaction is abolished when MBD1 is sumoylated (PubMed:15327775,
PubMed:17066076). Interacts with CBX1 and CBX5 (PubMed:15899859).
Interacts with DNMT3A and DNMT3B (PubMed:16682412). Interacts with
SUMO2. Interacts with CHD7, NLK1 and PPARG (PubMed:17952062).
Interacts with MPHOSPH8 (PubMed:20871592). Interacts with ERG (By
similarity). Interacts with HDAC1, HDAC2, SIN3A and SIN3B (By
similarity). Interacts with ATRX. Forms a complex with ATRX,
TRIM28 and ZNF274 (PubMed:27029610).
{ECO:0000250|UniProtKB:O88974, ECO:0000269|PubMed:11959841,
ECO:0000269|PubMed:14536086, ECO:0000269|PubMed:15327775,
ECO:0000269|PubMed:15691849, ECO:0000269|PubMed:15899859,
ECO:0000269|PubMed:16567619, ECO:0000269|PubMed:16682412,
ECO:0000269|PubMed:17066076, ECO:0000269|PubMed:17952062,
ECO:0000269|PubMed:19061646, ECO:0000269|PubMed:20871592,
ECO:0000269|PubMed:24623306, ECO:0000269|PubMed:27029610}.
-!- INTERACTION:
P31749:AKT1; NbExp=9; IntAct=EBI-79691, EBI-296087;
Q9Y6K1:DNMT3A; NbExp=7; IntAct=EBI-79691, EBI-923653;
Q9UIS9:MBD1; NbExp=3; IntAct=EBI-79691, EBI-867196;
Q99549:MPHOSPH8; NbExp=3; IntAct=EBI-79691, EBI-2653928;
Q8IUH5:ZDHHC17; NbExp=3; IntAct=EBI-9090795, EBI-524753;
-!- SUBCELLULAR LOCATION: Nucleus. Chromosome. Note=Associated with
non-pericentromeric regions of chromatin. Excluded from nucleoli
and islands of condensed chromatin.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=3;
Name=1;
IsoId=Q15047-1; Sequence=Displayed;
Name=2;
IsoId=Q15047-2; Sequence=VSP_002217, VSP_002218;
Note=No experimental confirmation available.;
Name=3;
IsoId=Q15047-3; Sequence=VSP_034600;
Note=No experimental confirmation available.;
-!- TISSUE SPECIFICITY: Widely expressed. High expression in testis.
-!- DOMAIN: The pre-SET, SET and post-SET domains are all required for
methyltransferase activity. The 347-amino-acid insertion in the
SET domain has no effect on the catalytic activity.
-!- DOMAIN: Isoform 2 lacks all domains required for histone
methyltransferase activity.
-!- DOMAIN: In the pre-SET domain, Cys residues bind 3 zinc ions that
are arranged in a triangular cluster; some of these Cys residues
contribute to the binding of two zinc ions within the cluster.
{ECO:0000250}.
-!- MISCELLANEOUS: Highly up-regulated in Huntington disease patients,
suggesting that participates in the altered chromatin modulation
and transcription dysfunction observed in Huntington disease. Its
down-regulation has salubrious effects on patients, suggesting
that it may be a promising treatment in Huntington disease
patients.
-!- SIMILARITY: Belongs to the class V-like SAM-binding
methyltransferase superfamily. Histone-lysine methyltransferase
family. Suvar3-9 subfamily. {ECO:0000255|PROSITE-
ProRule:PRU00906}.
-!- SEQUENCE CAUTION:
Sequence=BAA06689.2; Type=Erroneous initiation; Evidence={ECO:0000305};
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EMBL; D31891; BAA06689.2; ALT_INIT; mRNA.
EMBL; AL590133; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; CH471121; EAW53506.1; -; Genomic_DNA.
EMBL; BC009362; AAH09362.1; -; mRNA.
EMBL; BC028671; AAH28671.1; -; mRNA.
CCDS; CCDS44217.1; -. [Q15047-1]
CCDS; CCDS58026.1; -. [Q15047-2]
CCDS; CCDS972.1; -. [Q15047-3]
RefSeq; NP_001138887.1; NM_001145415.1. [Q15047-1]
RefSeq; NP_001230420.1; NM_001243491.1. [Q15047-2]
RefSeq; NP_036564.3; NM_012432.3. [Q15047-3]
RefSeq; XP_016858444.1; XM_017002955.1. [Q15047-2]
UniGene; Hs.643565; -.
PDB; 3DLM; X-ray; 1.77 A; A=196-402.
PDB; 4X3S; X-ray; 1.60 A; C/D=1165-1174.
PDB; 5KCH; X-ray; 1.70 A; A=196-403.
PDB; 5KCO; X-ray; 1.47 A; A=196-403.
PDB; 5KE2; X-ray; 1.56 A; A=196-402.
PDB; 5KE3; X-ray; 1.70 A; A=196-402.
PDB; 5KH6; X-ray; 2.05 A; A=196-400.
PDB; 6AU2; X-ray; 1.63 A; A=196-402.
PDB; 6AU3; X-ray; 1.80 A; A=196-402.
PDB; 6BHD; X-ray; 1.25 A; A=190-410.
PDB; 6BHE; X-ray; 1.35 A; A=190-410.
PDB; 6BHG; X-ray; 1.45 A; A=190-410.
PDB; 6BHH; X-ray; 1.85 A; A=190-410.
PDB; 6BHI; X-ray; 1.40 A; A=190-410.
PDB; 6BPI; X-ray; 1.64 A; A=196-402.
PDBsum; 3DLM; -.
PDBsum; 4X3S; -.
PDBsum; 5KCH; -.
PDBsum; 5KCO; -.
PDBsum; 5KE2; -.
PDBsum; 5KE3; -.
PDBsum; 5KH6; -.
PDBsum; 6AU2; -.
PDBsum; 6AU3; -.
PDBsum; 6BHD; -.
PDBsum; 6BHE; -.
PDBsum; 6BHG; -.
PDBsum; 6BHH; -.
PDBsum; 6BHI; -.
PDBsum; 6BPI; -.
ProteinModelPortal; Q15047; -.
SMR; Q15047; -.
BioGrid; 115202; 140.
CORUM; Q15047; -.
DIP; DIP-31029N; -.
IntAct; Q15047; 121.
MINT; Q15047; -.
STRING; 9606.ENSP00000271640; -.
BindingDB; Q15047; -.
ChEMBL; CHEMBL2321646; -.
iPTMnet; Q15047; -.
PhosphoSitePlus; Q15047; -.
BioMuta; SETDB1; -.
DMDM; 25091210; -.
EPD; Q15047; -.
MaxQB; Q15047; -.
PaxDb; Q15047; -.
PeptideAtlas; Q15047; -.
PRIDE; Q15047; -.
ProteomicsDB; 60397; -.
ProteomicsDB; 60398; -. [Q15047-2]
ProteomicsDB; 60399; -. [Q15047-3]
Ensembl; ENST00000271640; ENSP00000271640; ENSG00000143379. [Q15047-1]
Ensembl; ENST00000368962; ENSP00000357958; ENSG00000143379. [Q15047-2]
Ensembl; ENST00000368969; ENSP00000357965; ENSG00000143379. [Q15047-3]
GeneID; 9869; -.
KEGG; hsa:9869; -.
UCSC; uc001evu.3; human. [Q15047-1]
CTD; 9869; -.
DisGeNET; 9869; -.
EuPathDB; HostDB:ENSG00000143379.12; -.
GeneCards; SETDB1; -.
HGNC; HGNC:10761; SETDB1.
HPA; HPA018142; -.
HPA; HPA058484; -.
MIM; 604396; gene.
neXtProt; NX_Q15047; -.
OpenTargets; ENSG00000143379; -.
PharmGKB; PA35679; -.
eggNOG; KOG1141; Eukaryota.
eggNOG; COG2940; LUCA.
GeneTree; ENSGT00780000121845; -.
HOVERGEN; HBG061013; -.
InParanoid; Q15047; -.
KO; K11421; -.
OMA; TSMHQSR; -.
OrthoDB; EOG091G014F; -.
PhylomeDB; Q15047; -.
TreeFam; TF106411; -.
Reactome; R-HSA-3214841; PKMTs methylate histone lysines.
SIGNOR; Q15047; -.
ChiTaRS; SETDB1; human.
EvolutionaryTrace; Q15047; -.
GeneWiki; SETDB1; -.
GenomeRNAi; 9869; -.
PRO; PR:Q15047; -.
Proteomes; UP000005640; Chromosome 1.
Bgee; ENSG00000143379; Expressed in 215 organ(s), highest expression level in testis.
CleanEx; HS_SETDB1; -.
ExpressionAtlas; Q15047; baseline and differential.
Genevisible; Q15047; HS.
GO; GO:0005694; C:chromosome; IEA:UniProtKB-SubCell.
GO; GO:0005829; C:cytosol; IDA:HPA.
GO; GO:0043231; C:intracellular membrane-bounded organelle; IDA:HPA.
GO; GO:0005654; C:nucleoplasm; IDA:HPA.
GO; GO:0005634; C:nucleus; IDA:HPA.
GO; GO:0005886; C:plasma membrane; IDA:HPA.
GO; GO:0003682; F:chromatin binding; IDA:UniProtKB.
GO; GO:0003677; F:DNA binding; IEA:InterPro.
GO; GO:0018024; F:histone-lysine N-methyltransferase activity; IEA:UniProtKB-EC.
GO; GO:1990841; F:promoter-specific chromatin binding; IDA:UniProtKB.
GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
GO; GO:0090309; P:positive regulation of methylation-dependent chromatin silencing; IMP:UniProtKB.
GO; GO:0007265; P:Ras protein signal transduction; IMP:UniProtKB.
GO; GO:0045471; P:response to ethanol; IEA:Ensembl.
GO; GO:0033273; P:response to vitamin; IEA:Ensembl.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
InterPro; IPR016177; DNA-bd_dom_sf.
InterPro; IPR025796; Hist-Lys_N-MeTrfase_SETDB1.
InterPro; IPR001739; Methyl_CpG_DNA-bd.
InterPro; IPR003616; Post-SET_dom.
InterPro; IPR007728; Pre-SET_dom.
InterPro; IPR001214; SET_dom.
InterPro; IPR002999; Tudor.
Pfam; PF01429; MBD; 1.
Pfam; PF05033; Pre-SET; 1.
Pfam; PF00856; SET; 1.
SMART; SM00391; MBD; 1.
SMART; SM00468; PreSET; 1.
SMART; SM00317; SET; 1.
SMART; SM00333; TUDOR; 2.
SUPFAM; SSF54171; SSF54171; 1.
PROSITE; PS50982; MBD; 1.
PROSITE; PS50868; POST_SET; 1.
PROSITE; PS50867; PRE_SET; 1.
PROSITE; PS51573; SAM_MT43_SUVAR39_1; 1.
PROSITE; PS50280; SET; 1.
1: Evidence at protein level;
3D-structure; Alternative splicing; Chromatin regulator; Chromosome;
Coiled coil; Complete proteome; Isopeptide bond; Metal-binding;
Methylation; Methyltransferase; Nucleus; Phosphoprotein; Polymorphism;
Reference proteome; Repeat; Repressor; S-adenosyl-L-methionine;
Transcription; Transcription regulation; Transferase; Ubl conjugation;
Zinc.
CHAIN 1 1291 Histone-lysine N-methyltransferase
SETDB1.
/FTId=PRO_0000186064.
DOMAIN 257 320 Tudor 1.
DOMAIN 347 403 Tudor 2.
DOMAIN 594 665 MBD. {ECO:0000255|PROSITE-
ProRule:PRU00338}.
DOMAIN 727 800 Pre-SET. {ECO:0000255|PROSITE-
ProRule:PRU00157}.
DOMAIN 803 1266 SET. {ECO:0000255|PROSITE-
ProRule:PRU00190}.
DOMAIN 1275 1291 Post-SET. {ECO:0000255|PROSITE-
ProRule:PRU00155}.
REGION 813 815 S-adenosyl-L-methionine binding.
{ECO:0000250}.
REGION 1223 1224 S-adenosyl-L-methionine binding.
{ECO:0000250}.
COILED 18 64 {ECO:0000255}.
METAL 729 729 Zinc 1. {ECO:0000250}.
METAL 729 729 Zinc 2. {ECO:0000250}.
METAL 731 731 Zinc 1. {ECO:0000250}.
METAL 735 735 Zinc 1. {ECO:0000250}.
METAL 735 735 Zinc 3. {ECO:0000250}.
METAL 741 741 Zinc 1. {ECO:0000250}.
METAL 743 743 Zinc 2. {ECO:0000250}.
METAL 781 781 Zinc 2. {ECO:0000250}.
METAL 781 781 Zinc 3. {ECO:0000250}.
METAL 785 785 Zinc 2. {ECO:0000250}.
METAL 787 787 Zinc 3. {ECO:0000250}.
METAL 792 792 Zinc 3. {ECO:0000250}.
METAL 1226 1226 Zinc 4. {ECO:0000250}.
METAL 1279 1279 Zinc 4. {ECO:0000250}.
METAL 1281 1281 Zinc 4. {ECO:0000250}.
METAL 1286 1286 Zinc 4. {ECO:0000250}.
BINDING 851 851 S-adenosyl-L-methionine.
{ECO:0000255|PROSITE-ProRule:PRU00190}.
BINDING 853 853 S-adenosyl-L-methionine.
{ECO:0000255|PROSITE-ProRule:PRU00190}.
BINDING 1220 1220 S-adenosyl-L-methionine.
{ECO:0000255|PROSITE-ProRule:PRU00190}.
MOD_RES 112 112 Phosphoserine.
{ECO:0000250|UniProtKB:O88974}.
MOD_RES 117 117 Phosphoserine.
{ECO:0000250|UniProtKB:O88974}.
MOD_RES 120 120 Phosphothreonine.
{ECO:0000250|UniProtKB:O88974}.
MOD_RES 976 976 Phosphothreonine; by NLK.
{ECO:0000305|PubMed:17952062}.
MOD_RES 1025 1025 Phosphoserine.
{ECO:0000244|PubMed:23186163}.
MOD_RES 1066 1066 Phosphoserine.
{ECO:0000244|PubMed:18220336,
ECO:0000244|PubMed:18669648,
ECO:0000244|PubMed:21406692,
ECO:0000244|PubMed:23186163}.
MOD_RES 1170 1170 N6,N6,N6-trimethyllysine; alternate.
{ECO:0000244|PubMed:24129315}.
MOD_RES 1170 1170 N6,N6-dimethyllysine; alternate.
{ECO:0000244|PubMed:24129315}.
MOD_RES 1178 1178 N6,N6,N6-trimethyllysine; alternate.
{ECO:0000244|PubMed:24129315}.
MOD_RES 1178 1178 N6,N6-dimethyllysine; alternate.
{ECO:0000244|PubMed:24129315}.
CROSSLNK 182 182 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in SUMO2);
alternate. {ECO:0000244|PubMed:28112733}.
CROSSLNK 182 182 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in ubiquitin);
alternate.
CROSSLNK 1032 1032 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in SUMO1);
alternate. {ECO:0000244|PubMed:25114211}.
CROSSLNK 1032 1032 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in SUMO2);
alternate. {ECO:0000244|PubMed:25218447,
ECO:0000244|PubMed:25755297,
ECO:0000244|PubMed:25772364,
ECO:0000244|PubMed:28112733}.
CROSSLNK 1038 1038 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in SUMO2).
{ECO:0000244|PubMed:28112733}.
CROSSLNK 1069 1069 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in SUMO2).
{ECO:0000244|PubMed:25218447,
ECO:0000244|PubMed:25755297,
ECO:0000244|PubMed:25772364,
ECO:0000244|PubMed:28112733}.
CROSSLNK 1149 1149 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in SUMO2).
{ECO:0000244|PubMed:28112733}.
VAR_SEQ 381 397 DDKRCEWIYRGSTRLEP -> VLFFSTILEAEVGGGGT
(in isoform 2).
{ECO:0000303|PubMed:15489334}.
/FTId=VSP_002217.
VAR_SEQ 398 1291 Missing (in isoform 2).
{ECO:0000303|PubMed:15489334}.
/FTId=VSP_002218.
VAR_SEQ 1254 1254 Missing (in isoform 3).
{ECO:0000303|PubMed:15489334}.
/FTId=VSP_034600.
VARIANT 236 236 N -> S (in dbSNP:rs2271075).
/FTId=VAR_014284.
VARIANT 506 506 P -> S (in dbSNP:rs17852587).
{ECO:0000269|PubMed:15489334}.
/FTId=VAR_031281.
VARIANT 824 824 A -> G (in dbSNP:rs2691551).
/FTId=VAR_014286.
VARIANT 824 824 A -> P (in dbSNP:rs2814054).
/FTId=VAR_014285.
MUTAGEN 729 731 CDC->LDP: Abolishes methyltransferase
activity. {ECO:0000269|PubMed:11959841}.
MUTAGEN 976 976 T->A: Abrogates interaction with CHD7,
NLK and PPARG. Reduces phosphorylation by
NLK. Reduces transcriptional repression.
{ECO:0000269|PubMed:17952062}.
MUTAGEN 1224 1224 H->K: Abolishes methyltransferase
activity. {ECO:0000269|PubMed:11959841}.
MUTAGEN 1226 1226 C->A: Abolishes methyltransferase
activity. {ECO:0000269|PubMed:11959841}.
MUTAGEN 1279 1279 C->Y: Abolishes methyltransferase
activity. {ECO:0000269|PubMed:11959841}.
STRAND 191 195 {ECO:0000244|PDB:6BHD}.
STRAND 203 207 {ECO:0000244|PDB:6BHD}.
STRAND 213 224 {ECO:0000244|PDB:6BHD}.
STRAND 227 237 {ECO:0000244|PDB:6BHD}.
STRAND 239 242 {ECO:0000244|PDB:6BHD}.
HELIX 244 246 {ECO:0000244|PDB:6BHD}.
STRAND 247 251 {ECO:0000244|PDB:6BHD}.
HELIX 255 257 {ECO:0000244|PDB:6BHE}.
STRAND 263 269 {ECO:0000244|PDB:6BHD}.
STRAND 274 283 {ECO:0000244|PDB:6BHD}.
TURN 287 290 {ECO:0000244|PDB:6BHD}.
STRAND 293 297 {ECO:0000244|PDB:6BHD}.
STRAND 302 305 {ECO:0000244|PDB:6BHD}.
HELIX 307 309 {ECO:0000244|PDB:6BHD}.
STRAND 310 315 {ECO:0000244|PDB:6BHD}.
HELIX 320 323 {ECO:0000244|PDB:6BHD}.
HELIX 327 339 {ECO:0000244|PDB:6BHD}.
STRAND 353 358 {ECO:0000244|PDB:6BHD}.
STRAND 361 371 {ECO:0000244|PDB:6BHD}.
STRAND 374 379 {ECO:0000244|PDB:6BHD}.
TURN 380 383 {ECO:0000244|PDB:6BHD}.
STRAND 384 389 {ECO:0000244|PDB:6BHD}.
HELIX 396 403 {ECO:0000244|PDB:6BHD}.
STRAND 1167 1172 {ECO:0000244|PDB:4X3S}.
SEQUENCE 1291 AA; 143157 MW; D8841B4C41B911C5 CRC64;
MSSLPGCIGL DAATATVESE EIAELQQAVV EELGISMEEL RHFIDEELEK MDCVQQRKKQ
LAELETWVIQ KESEVAHVDQ LFDDASRAVT NCESLVKDFY SKLGLQYRDS SSEDESSRPT
EIIEIPDEDD DVLSIDSGDA GSRTPKDQKL REAMAALRKS AQDVQKFMDA VNKKSSSQDL
HKGTLSQMSG ELSKDGDLIV SMRILGKKRT KTWHKGTLIA IQTVGPGKKY KVKFDNKGKS
LLSGNHIAYD YHPPADKLYV GSRVVAKYKD GNQVWLYAGI VAETPNVKNK LRFLIFFDDG
YASYVTQSEL YPICRPLKKT WEDIEDISCR DFIEEYVTAY PNRPMVLLKS GQLIKTEWEG
TWWKSRVEEV DGSLVRILFL DDKRCEWIYR GSTRLEPMFS MKTSSASALE KKQGQLRTRP
NMGAVRSKGP VVQYTQDLTG TGTQFKPVEP PQPTAPPAPP FPPAPPLSPQ AGDSDLESQL
AQSRKQVAKK STSFRPGSVG SGHSSPTSPA LSENVSGGKP GINQTYRSPL GSTASAPAPS
ALPAPPAPPV FHGMLERAPA EPSYRAPMEK LFYLPHVCSY TCLSRVRPMR NEQYRGKNPL
LVPLLYDFRR MTARRRVNRK MGFHVIYKTP CGLCLRTMQE IERYLFETGC DFLFLEMFCL
DPYVLVDRKF QPYKPFYYIL DITYGKEDVP LSCVNEIDTT PPPQVAYSKE RIPGKGVFIN
TGPEFLVGCD CKDGCRDKSK CACHQLTIQA TACTPGGQIN PNSGYQYKRL EECLPTGVYE
CNKRCKCDPN MCTNRLVQHG LQVRLQLFKT QNKGWGIRCL DDIAKGSFVC IYAGKILTDD
FADKEGLEMG DEYFANLDHI ESVENFKEGY ESDAPCSSDS SGVDLKDQED GNSGTEDPEE
SNDDSSDDNF CKDEDFSTSS VWRSYATRRQ TRGQKENGLS ETTSKDSHPP DLGPPHIPVP
PSIPVGGCNP PSSEETPKNK VASWLSCNSV SEGGFADSDS HSSFKTNEGG EGRAGGSRME
AEKASTSGLG IKDEGDIKQA KKEDTDDRNK MSVVTESSRN YGYNPSPVKP EGLRRPPSKT
SMHQSRRLMA SAQSNPDDVL TLSSSTESEG ESGTSRKPTA GQTSATAVDS DDIQTISSGS
EGDDFEDKKN MTGPMKRQVA VKSTRGFALK STHGIAIKST NMASVDKGES APVRKNTRQF
YDGEESCYII DAKLEGNLGR YLNHSCSPNL FVQNVFVDTH DLRFPWVAFF ASKRIRAGTE
LTWDYNYEVG SVEGKELLCC CGAIECRGRL L


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