SUV39_DROME
ID SUV39_DROME Reviewed; 635 AA.
AC P45975; Q9VFA6;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 21-NOV-2003, sequence version 2.
DT 03-AUG-2022, entry version 205.
DE RecName: Full=Histone-lysine N-methyltransferase Su(var)3-9;
DE EC=2.1.1.355 {ECO:0000269|PubMed:11867540};
DE AltName: Full=Histone H3-K9 methyltransferase;
DE Short=H3-K9-HMTase;
DE AltName: Full=Lysine N-methyltransferase 1;
DE AltName: Full=Protein suppressor of variegation 3-9;
GN Name=Su(var)3-9; Synonyms=KMT1; ORFNames=CG6476;
OS Drosophila melanogaster (Fruit fly).
OC Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea;
OC Drosophilidae; Drosophila; Sophophora.
OX NCBI_TaxID=7227;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND DEVELOPMENTAL STAGE.
RC STRAIN=Oregon-R;
RX PubMed=7915232; DOI=10.1002/j.1460-2075.1994.tb06693.x;
RA Tschiersch B., Hofmann A., Krauss V., Dorn R., Korge G., Reuter G.;
RT "The protein encoded by the Drosophila position-effect variegation
RT suppressor gene Su(var)3-9 combines domains of antagonistic regulators of
RT homeotic gene complexes.";
RL EMBO J. 13:3822-3831(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=Karsnas;
RX PubMed=11063691; DOI=10.1093/genetics/156.3.1157;
RA Krauss V., Reuter G.;
RT "Two genes become one: the genes encoding heterochromatin protein Su(var)3-
RT 9 and translation initiation factor subunit eIF-2gamma are joined to a
RT dicistronic unit in holometabolic insects.";
RL Genetics 156:1157-1167(2000).
RN [3]
RP SEQUENCE REVISION TO 509.
RA Schotta G., Ebert A., Lein S., Kubicek S., Krauss V., Jenuwein T.,
RA Reuter F.;
RT "Histone H3-K9 methylation potential of Drosophila Su(var)3-9 mutants
RT correlates with extent of gene silencing.";
RL Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Berkeley;
RX PubMed=10731132; DOI=10.1126/science.287.5461.2185;
RA Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
RA Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
RA George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
RA Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X., Brandon R.C.,
RA Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C.,
RA Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A.,
RA An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A.,
RA Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V.,
RA Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J.,
RA Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E.,
RA Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B.,
RA Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I.,
RA Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C.,
RA Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S.,
RA Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M.,
RA Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M.,
RA Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D.,
RA Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F.,
RA Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D.,
RA Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A.,
RA Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C.,
RA McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C.,
RA Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L.,
RA Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R.,
RA Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V.,
RA Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F.,
RA Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J.,
RA Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R.,
RA Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y.,
RA Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T.,
RA Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S.,
RA Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W.,
RA Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M.,
RA Venter J.C.;
RT "The genome sequence of Drosophila melanogaster.";
RL Science 287:2185-2195(2000).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=Berkeley;
RX PubMed=12537572; DOI=10.1186/gb-2002-3-12-research0083;
RA Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S.,
RA Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E.,
RA Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P.,
RA Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A.,
RA Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q., Stapleton M.,
RA Yamada C., Ashburner M., Gelbart W.M., Rubin G.M., Lewis S.E.;
RT "Annotation of the Drosophila melanogaster euchromatic genome: a systematic
RT review.";
RL Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
RN [6]
RP INTERACTION WITH HDAC1.
RX PubMed=11571273; DOI=10.1093/embo-reports/kve210;
RA Czermin B., Schotta G., Huelsmann B.B., Brehm A., Becker P.B., Reuter G.,
RA Imhof A.;
RT "Physical and functional association of SU(VAR)3-9 and HDAC1 in
RT Drosophila.";
RL EMBO Rep. 2:915-919(2001).
RN [7]
RP CATALYTIC ACTIVITY, AND INTERACTION WITH SU(VAR)205 AND SU(VAR)3-7.
RX PubMed=11867540; DOI=10.1093/emboj/21.5.1121;
RA Schotta G., Ebert A., Krauss V., Fischer A., Hoffmann J., Rea S.,
RA Jenuwein T., Dorn R., Reuter G.;
RT "Central role of Drosophila SU(VAR)3-9 in histone H3-K9 methylation and
RT heterochromatic gene silencing.";
RL EMBO J. 21:1121-1131(2002).
RN [8]
RP FUNCTION.
RX PubMed=14630943; DOI=10.1101/gad.281503;
RA Greil F., van der Kraan I., Delrow J., Smothers J.F., de Wit E.,
RA Bussemaker H.J., van Driel R., Henikoff S., van Steensel B.;
RT "Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally
RT coexpressed genes depending on chromosomal location.";
RL Genes Dev. 17:2825-2838(2003).
CC -!- FUNCTION: Histone methyltransferase that specifically trimethylates
CC 'Lys-9' of histone H3 using monomethylated H3 'Lys-9' as substrate. H3
CC 'Lys-9' trimethylation represents a specific tag for epigenetic
CC transcriptional repression by recruiting Su(var)205/HP1 to methylated
CC histones. Mainly functions in heterochromatin regions, thereby playing
CC a central role in the establishment of constitutive heterochromatin at
CC pericentric regions. Involved in heterochromatic gene silencing
CC including the modification of position-effect-variegation.
CC {ECO:0000269|PubMed:14630943}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-lysyl(9)-[histone H3] + 3 S-adenosyl-L-methionine = 3 H(+) +
CC N(6),N(6),N(6)-trimethyl-L-lysyl(9)-[histone H3] + 3 S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:60276, Rhea:RHEA-COMP:15538, Rhea:RHEA-
CC COMP:15546, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856,
CC ChEBI:CHEBI:59789, ChEBI:CHEBI:61961; EC=2.1.1.355;
CC Evidence={ECO:0000269|PubMed:11867540};
CC -!- SUBUNIT: Interacts with Su(var)205 and Su(var)3-7. Probably associates
CC with HDAC1/Rpd3. {ECO:0000269|PubMed:11571273,
CC ECO:0000269|PubMed:11867540}.
CC -!- INTERACTION:
CC P45975; P02255: His1:CG33843; NbExp=4; IntAct=EBI-110378, EBI-151629;
CC P45975; P05205: Su(var)205; NbExp=3; IntAct=EBI-110378, EBI-155532;
CC -!- SUBCELLULAR LOCATION: Nucleus. Chromosome, centromere. Note=Associates
CC with centromeric constitutive heterochromatin.
CC -!- DEVELOPMENTAL STAGE: Expressed maternally and zygotically. Expressed
CC throughout development with a peak of expression during early
CC embryogenesis (0-9 hours old embryos). Weak expression in larvae, pupae
CC and adult flies. {ECO:0000269|PubMed:7915232}.
CC -!- DOMAIN: Although the SET domain contains the active site of enzymatic
CC activity, both pre-SET and post-SET domains are required for
CC methyltransferase activity. The SET domain also participates in stable
CC binding to heterochromatin (By similarity). {ECO:0000250}.
CC -!- DOMAIN: In the pre-SET domain, Cys residues bind 3 zinc ions that are
CC arranged in a triangular cluster; some of these Cys residues contribute
CC to the binding of two zinc ions within the cluster. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the class V-like SAM-binding methyltransferase
CC superfamily. Histone-lysine methyltransferase family. Suvar3-9
CC subfamily. {ECO:0000255|PROSITE-ProRule:PRU00190}.
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DR EMBL; X80070; CAA56376.1; -; mRNA.
DR EMBL; AJ290956; CAB93768.2; -; Genomic_DNA.
DR EMBL; AE014297; AAF55154.1; -; Genomic_DNA.
DR PIR; S47004; S47004.
DR RefSeq; NP_524357.2; NM_079633.3.
DR AlphaFoldDB; P45975; -.
DR SMR; P45975; -.
DR BioGRID; 66596; 41.
DR DIP; DIP-23970N; -.
DR IntAct; P45975; 4.
DR MINT; P45975; -.
DR STRING; 7227.FBpp0302536; -.
DR BindingDB; P45975; -.
DR ChEMBL; CHEMBL2169720; -.
DR PaxDb; P45975; -.
DR PRIDE; P45975; -.
DR GeneID; 41483; -.
DR KEGG; dme:Dmel_CG43664; -.
DR CTD; 41483; -.
DR FlyBase; FBgn0263755; Su(var)3-9.
DR VEuPathDB; VectorBase:FBgn0263755; -.
DR eggNOG; KOG1082; Eukaryota.
DR HOGENOM; CLU_020840_8_1_1; -.
DR InParanoid; P45975; -.
DR PhylomeDB; P45975; -.
DR Reactome; R-DME-427359; SIRT1 negatively regulates rRNA expression.
DR SABIO-RK; P45975; -.
DR SignaLink; P45975; -.
DR BioGRID-ORCS; 41483; 1 hit in 3 CRISPR screens.
DR GenomeRNAi; 41483; -.
DR PRO; PR:P45975; -.
DR Proteomes; UP000000803; Chromosome 3R.
DR ExpressionAtlas; P45975; baseline and differential.
DR Genevisible; P45975; DM.
DR GO; GO:0000775; C:chromosome, centromeric region; TAS:FlyBase.
DR GO; GO:0000781; C:chromosome, telomeric region; IEA:GOC.
DR GO; GO:0000792; C:heterochromatin; IDA:FlyBase.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0005701; C:polytene chromosome chromocenter; IDA:FlyBase.
DR GO; GO:0003682; F:chromatin binding; IDA:FlyBase.
DR GO; GO:0042054; F:histone methyltransferase activity; IDA:UniProtKB.
DR GO; GO:0046974; F:histone methyltransferase activity (H3-K9 specific); IDA:FlyBase.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0006325; P:chromatin organization; IMP:FlyBase.
DR GO; GO:0051276; P:chromosome organization; IMP:FlyBase.
DR GO; GO:0006306; P:DNA methylation; IMP:FlyBase.
DR GO; GO:0048132; P:female germ-line stem cell asymmetric division; IDA:FlyBase.
DR GO; GO:0080188; P:gene silencing by RNA-directed DNA methylation; IMP:FlyBase.
DR GO; GO:0031507; P:heterochromatin assembly; IMP:FlyBase.
DR GO; GO:0070828; P:heterochromatin organization; IMP:FlyBase.
DR GO; GO:0051567; P:histone H3-K9 methylation; IDA:FlyBase.
DR GO; GO:0034968; P:histone lysine methylation; IBA:GO_Central.
DR GO; GO:0016571; P:histone methylation; IDA:FlyBase.
DR GO; GO:0016570; P:histone modification; IMP:FlyBase.
DR GO; GO:2001229; P:negative regulation of response to gamma radiation; IMP:FlyBase.
DR GO; GO:0048477; P:oogenesis; IDA:FlyBase.
DR GO; GO:0031508; P:pericentric heterochromatin assembly; HMP:FlyBase.
DR GO; GO:0031509; P:subtelomeric heterochromatin assembly; HMP:FlyBase.
DR Gene3D; 2.170.270.10; -; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR016197; Chromo-like_dom_sf.
DR InterPro; IPR000953; Chromo/chromo_shadow_dom.
DR InterPro; IPR023780; Chromo_domain.
DR InterPro; IPR023779; Chromodomain_CS.
DR InterPro; IPR011381; Histone_H3-K9_MeTrfase.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR003616; Post-SET_dom.
DR InterPro; IPR007728; Pre-SET_dom.
DR InterPro; IPR001214; SET_dom.
DR InterPro; IPR046341; SET_dom_sf.
DR Pfam; PF00385; Chromo; 1.
DR Pfam; PF05033; Pre-SET; 1.
DR Pfam; PF00856; SET; 1.
DR PIRSF; PIRSF009343; SUV39_SET; 1.
DR SMART; SM00298; CHROMO; 1.
DR SMART; SM00468; PreSET; 1.
DR SMART; SM00317; SET; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR SUPFAM; SSF54160; SSF54160; 1.
DR SUPFAM; SSF82199; SSF82199; 1.
DR PROSITE; PS00598; CHROMO_1; 1.
DR PROSITE; PS50013; CHROMO_2; 1.
DR PROSITE; PS50868; POST_SET; 1.
DR PROSITE; PS50867; PRE_SET; 1.
DR PROSITE; PS50280; SET; 1.
PE 1: Evidence at protein level;
KW Centromere; Chromatin regulator; Chromosome; Metal-binding;
KW Methyltransferase; Nucleus; Reference proteome; Repressor;
KW S-adenosyl-L-methionine; Transcription; Transcription regulation;
KW Transferase; Zinc.
FT CHAIN 1..635
FT /note="Histone-lysine N-methyltransferase Su(var)3-9"
FT /id="PRO_0000186061"
FT DOMAIN 219..278
FT /note="Chromo"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00053"
FT DOMAIN 410..474
FT /note="Pre-SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00157"
FT DOMAIN 477..603
FT /note="SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT DOMAIN 619..635
FT /note="Post-SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00155"
FT REGION 81..188
FT /note="Binds to Su(var)205 and Suvar(3)7"
FT REGION 123..161
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 191..210
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 125..161
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 412
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 412
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 414
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 421
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 421
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250"
FT BINDING 427
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 428
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 428
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 456
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 456
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250"
FT BINDING 460
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 462
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250"
FT BINDING 466
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250"
FT BINDING 488..490
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 531
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT BINDING 560..561
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 563
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250"
FT BINDING 623
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250"
FT BINDING 625
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250"
FT BINDING 630
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250"
FT CONFLICT 275
FT /note="T -> I (in Ref. 4; AAF55154)"
FT /evidence="ECO:0000305"
FT CONFLICT 509
FT /note="G -> E (in Ref. 1; CAA56376)"
FT /evidence="ECO:0000305"
FT CONFLICT 627
FT /note="R -> A (in Ref. 4; AAF55154)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 635 AA; 71904 MW; 4154A49F54B60E14 CRC64;
MATAEAQIGV NRNLQKQDLS NLDVSKLTPL SPEVISRQAT INIGTIGHVA HGKSTVVKAI
SGVQTVRFKN ELERNITIKL ERLSEKKIKN LLTSKQQRQQ YEIKQRSMLR HLAELRRHSR
FRRLCTKPAS SSMPASTSSV DRRTTRRSTS QTSLSPSNSS GYGSVFGCEE HDVDKIPSLN
GFAKLKRRRS SCVGAPTPNS KRSKNNMGVI AKRPPKGEYV VERIECVEMD QYQPVFFVKW
LGYHDSENTW ESLANVADCA EMEKFVERHQ QLYETYIAKI TTELEKQLEA LPLMENITVA
EVDAYEPLNL QIDLILLAQY RAAGSRSQRE PQKIGERALK SMQIKRAQFV RRKQLADLAL
FEKRMNHVEK PSPPIRVENN IDLDTIDSNF MYIHDNIIGK DVPKPEAGIV GCKCTEDTEE
CTASTKCCAR FAGELFAYER STRRLRLRPG SAIYECNSRC SCDSSCSNRL VQHGRQVPLV
LFKTANGSGW GVRAATALRK GEFVCEYIGE IITSDEANER GKAYDDNGRT YLFDLDYNTA
QDSEYTIDAA NYGNISHFIN HSCDPNLAVF PCWIEHLNVA LPHLVFFTLR PIKAGEELSF
DYIRADNEDV PYENLSTAVR VECRCGRDNC RKVLF
