Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Histone-lysine N-methyltransferase Su(var)3-9

Gene

Su(var)3-9

Organism
Drosophila melanogaster (Fruit fly)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Histone methyltransferase that specifically trimethylates 'Lys-9' of histone H3 using monomethylated H3 'Lys-9' as substrate. H3 'Lys-9' trimethylation represents a specific tag for epigenetic transcriptional repression by recruiting Su(var)205/HP1 to methylated histones. Mainly functions in heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin at pericentric regions. Involved in heterochromatic gene silencing including the modification of position-effect-variegation.1 Publication

Catalytic activityi

S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi412 – 4121Zinc 1By similarity
Metal bindingi412 – 4121Zinc 2By similarity
Metal bindingi414 – 4141Zinc 1By similarity
Metal bindingi421 – 4211Zinc 1By similarity
Metal bindingi421 – 4211Zinc 3By similarity
Metal bindingi427 – 4271Zinc 1By similarity
Metal bindingi428 – 4281Zinc 1By similarity
Metal bindingi428 – 4281Zinc 2By similarity
Metal bindingi456 – 4561Zinc 2By similarity
Metal bindingi456 – 4561Zinc 3By similarity
Metal bindingi460 – 4601Zinc 2By similarity
Metal bindingi462 – 4621Zinc 3By similarity
Metal bindingi466 – 4661Zinc 3By similarity
Binding sitei531 – 5311S-adenosyl-L-methioninePROSITE-ProRule annotation
Metal bindingi563 – 5631Zinc 4By similarity
Metal bindingi623 – 6231Zinc 4By similarity
Metal bindingi625 – 6251Zinc 4By similarity
Metal bindingi630 – 6301Zinc 4By similarity

GO - Molecular functioni

  • chromatin binding Source: FlyBase
  • histone methyltransferase activity Source: UniProtKB
  • histone methyltransferase activity (H3-K9 specific) Source: FlyBase
  • zinc ion binding Source: InterPro

GO - Biological processi

  • chromatin organization Source: FlyBase
  • chromatin silencing Source: FlyBase
  • chromatin silencing at centromere Source: FlyBase
  • chromatin silencing at telomere Source: FlyBase
  • chromosome organization Source: FlyBase
  • DNA methylation Source: FlyBase
  • female germ-line stem cell asymmetric division Source: FlyBase
  • gene silencing Source: UniProtKB
  • heterochromatin assembly Source: FlyBase
  • heterochromatin organization involved in chromatin silencing Source: FlyBase
  • histone H3-K9 methylation Source: FlyBase
  • histone methylation Source: FlyBase
  • histone modification Source: FlyBase
  • negative regulation of response to gamma radiation Source: FlyBase
  • oogenesis Source: FlyBase
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Methyltransferase, Repressor, Transferase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

Metal-binding, S-adenosyl-L-methionine, Zinc

Enzyme and pathway databases

ReactomeiR-DME-3214841. PKMTs methylate histone lysines.
SABIO-RKP45975.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone-lysine N-methyltransferase Su(var)3-9 (EC:2.1.1.43)
Alternative name(s):
Histone H3-K9 methyltransferase
Short name:
H3-K9-HMTase
Lysine N-methyltransferase 1
Protein suppressor of variegation 3-9
Gene namesi
Name:Su(var)3-9
Synonyms:KMT1
ORF Names:CG6476
OrganismiDrosophila melanogaster (Fruit fly)
Taxonomic identifieri7227 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaArthropodaHexapodaInsectaPterygotaNeopteraEndopterygotaDipteraBrachyceraMuscomorphaEphydroideaDrosophilidaeDrosophilaSophophora
Proteomesi
  • UP000000803 Componenti: Chromosome 3R

Organism-specific databases

FlyBaseiFBgn0263755. Su(var)3-9.

Subcellular locationi

GO - Cellular componenti

  • chromosome, centromeric region Source: FlyBase
  • chromosome, telomeric region Source: GOC
  • heterochromatin Source: FlyBase
  • nucleus Source: FlyBase
  • polytene chromosome chromocenter Source: FlyBase
Complete GO annotation...

Keywords - Cellular componenti

Centromere, Chromosome, Nucleus

Pathology & Biotechi

Chemistry

ChEMBLiCHEMBL2169720.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 635635Histone-lysine N-methyltransferase Su(var)3-9PRO_0000186061Add
BLAST

Proteomic databases

PaxDbiP45975.
PRIDEiP45975.

Expressioni

Developmental stagei

Expressed maternally and zygotically. Expressed throughout development with a peak of expression during early embryogenesis (0-9 hours old embryos). Weak expression in larvae, pupae and adult flies.1 Publication

Gene expression databases

BgeeiP45975.
ExpressionAtlasiP45975. differential.
GenevisibleiP45975. DM.

Interactioni

Subunit structurei

Interacts with Su(var)205 and Su(var)3-7. Probably associates with Rpd3.2 Publications

Protein-protein interaction databases

BioGridi66596. 24 interactions.
DIPiDIP-23970N.
IntActiP45975. 2 interactions.
MINTiMINT-748988.
STRINGi7227.FBpp0302536.

Chemistry

BindingDBiP45975.

Structurei

3D structure databases

ProteinModelPortaliP45975.
SMRiP45975. Positions 38-98, 233-258, 347-634.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini219 – 27860ChromoPROSITE-ProRule annotationAdd
BLAST
Domaini410 – 47465Pre-SETPROSITE-ProRule annotationAdd
BLAST
Domaini477 – 603127SETPROSITE-ProRule annotationAdd
BLAST
Domaini619 – 63517Post-SETPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni81 – 188108Binds to Su(var)205 and Suvar(3)7Add
BLAST
Regioni488 – 4903S-adenosyl-L-methionine bindingBy similarity
Regioni560 – 5612S-adenosyl-L-methionine bindingBy similarity

Domaini

Although the SET domain contains the active site of enzymatic activity, both pre-SET and post-SET domains are required for methyltransferase activity. The SET domain also participates to stable binding to heterochromatin (By similarity).By similarity
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.By similarity

Sequence similaritiesi

Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. Suvar3-9 subfamily.PROSITE-ProRule annotation
Contains 1 chromo domain.PROSITE-ProRule annotation
Contains 1 post-SET domain.PROSITE-ProRule annotation
Contains 1 pre-SET domain.PROSITE-ProRule annotation
Contains 1 SET domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG1082. Eukaryota.
COG2940. LUCA.
COG5257. LUCA.
InParanoidiP45975.
KOiK11419.
PhylomeDBiP45975.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR000953. Chromo/shadow_dom.
IPR023780. Chromo_domain.
IPR016197. Chromodomain-like.
IPR023779. Chromodomain_CS.
IPR011381. Histone_H3-K9_MeTrfase.
IPR027417. P-loop_NTPase.
IPR003616. Post-SET_dom.
IPR007728. Pre-SET_dom.
IPR001214. SET_dom.
[Graphical view]
PfamiPF00385. Chromo. 1 hit.
PF05033. Pre-SET. 1 hit.
PF00856. SET. 1 hit.
[Graphical view]
PIRSFiPIRSF009343. SUV39_SET. 1 hit.
SMARTiSM00298. CHROMO. 1 hit.
SM00468. PreSET. 1 hit.
SM00317. SET. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
SSF54160. SSF54160. 1 hit.
PROSITEiPS00598. CHROMO_1. 1 hit.
PS50013. CHROMO_2. 1 hit.
PS50868. POST_SET. 1 hit.
PS50867. PRE_SET. 1 hit.
PS50280. SET. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P45975-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MATAEAQIGV NRNLQKQDLS NLDVSKLTPL SPEVISRQAT INIGTIGHVA
60 70 80 90 100
HGKSTVVKAI SGVQTVRFKN ELERNITIKL ERLSEKKIKN LLTSKQQRQQ
110 120 130 140 150
YEIKQRSMLR HLAELRRHSR FRRLCTKPAS SSMPASTSSV DRRTTRRSTS
160 170 180 190 200
QTSLSPSNSS GYGSVFGCEE HDVDKIPSLN GFAKLKRRRS SCVGAPTPNS
210 220 230 240 250
KRSKNNMGVI AKRPPKGEYV VERIECVEMD QYQPVFFVKW LGYHDSENTW
260 270 280 290 300
ESLANVADCA EMEKFVERHQ QLYETYIAKI TTELEKQLEA LPLMENITVA
310 320 330 340 350
EVDAYEPLNL QIDLILLAQY RAAGSRSQRE PQKIGERALK SMQIKRAQFV
360 370 380 390 400
RRKQLADLAL FEKRMNHVEK PSPPIRVENN IDLDTIDSNF MYIHDNIIGK
410 420 430 440 450
DVPKPEAGIV GCKCTEDTEE CTASTKCCAR FAGELFAYER STRRLRLRPG
460 470 480 490 500
SAIYECNSRC SCDSSCSNRL VQHGRQVPLV LFKTANGSGW GVRAATALRK
510 520 530 540 550
GEFVCEYIGE IITSDEANER GKAYDDNGRT YLFDLDYNTA QDSEYTIDAA
560 570 580 590 600
NYGNISHFIN HSCDPNLAVF PCWIEHLNVA LPHLVFFTLR PIKAGEELSF
610 620 630
DYIRADNEDV PYENLSTAVR VECRCGRDNC RKVLF
Length:635
Mass (Da):71,904
Last modified:November 21, 2003 - v2
Checksum:i4154A49F54B60E14
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti275 – 2751T → I in AAF55154 (PubMed:10731132).Curated
Sequence conflicti509 – 5091G → E in CAA56376 (PubMed:7915232).Curated
Sequence conflicti627 – 6271R → A in AAF55154 (PubMed:10731132).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X80070 mRNA. Translation: CAA56376.1.
AJ290956 Genomic DNA. Translation: CAB93768.2.
AE014297 Genomic DNA. Translation: AAF55154.1.
PIRiS47004.
RefSeqiNP_524357.2. NM_079633.3.
UniGeneiDm.3299.

Genome annotation databases

GeneIDi41483.
KEGGidme:Dmel_CG43664.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X80070 mRNA. Translation: CAA56376.1.
AJ290956 Genomic DNA. Translation: CAB93768.2.
AE014297 Genomic DNA. Translation: AAF55154.1.
PIRiS47004.
RefSeqiNP_524357.2. NM_079633.3.
UniGeneiDm.3299.

3D structure databases

ProteinModelPortaliP45975.
SMRiP45975. Positions 38-98, 233-258, 347-634.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi66596. 24 interactions.
DIPiDIP-23970N.
IntActiP45975. 2 interactions.
MINTiMINT-748988.
STRINGi7227.FBpp0302536.

Chemistry

BindingDBiP45975.
ChEMBLiCHEMBL2169720.

Proteomic databases

PaxDbiP45975.
PRIDEiP45975.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi41483.
KEGGidme:Dmel_CG43664.

Organism-specific databases

CTDi41483.
FlyBaseiFBgn0263755. Su(var)3-9.

Phylogenomic databases

eggNOGiKOG1082. Eukaryota.
COG2940. LUCA.
COG5257. LUCA.
InParanoidiP45975.
KOiK11419.
PhylomeDBiP45975.

Enzyme and pathway databases

ReactomeiR-DME-3214841. PKMTs methylate histone lysines.
SABIO-RKP45975.

Miscellaneous databases

GenomeRNAii41483.
NextBioi825848.
PROiP45975.

Gene expression databases

BgeeiP45975.
ExpressionAtlasiP45975. differential.
GenevisibleiP45975. DM.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR000953. Chromo/shadow_dom.
IPR023780. Chromo_domain.
IPR016197. Chromodomain-like.
IPR023779. Chromodomain_CS.
IPR011381. Histone_H3-K9_MeTrfase.
IPR027417. P-loop_NTPase.
IPR003616. Post-SET_dom.
IPR007728. Pre-SET_dom.
IPR001214. SET_dom.
[Graphical view]
PfamiPF00385. Chromo. 1 hit.
PF05033. Pre-SET. 1 hit.
PF00856. SET. 1 hit.
[Graphical view]
PIRSFiPIRSF009343. SUV39_SET. 1 hit.
SMARTiSM00298. CHROMO. 1 hit.
SM00468. PreSET. 1 hit.
SM00317. SET. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
SSF54160. SSF54160. 1 hit.
PROSITEiPS00598. CHROMO_1. 1 hit.
PS50013. CHROMO_2. 1 hit.
PS50868. POST_SET. 1 hit.
PS50867. PRE_SET. 1 hit.
PS50280. SET. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The protein encoded by the Drosophila position-effect variegation suppressor gene Su(var)3-9 combines domains of antagonistic regulators of homeotic gene complexes."
    Tschiersch B., Hofmann A., Krauss V., Dorn R., Korge G., Reuter G.
    EMBO J. 13:3822-3831(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], DEVELOPMENTAL STAGE.
    Strain: Oregon-R.
  2. "Two genes become one: the genes encoding heterochromatin protein Su(var)3-9 and translation initiation factor subunit eIF-2gamma are joined to a dicistronic unit in holometabolic insects."
    Krauss V., Reuter G.
    Genetics 156:1157-1167(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: Karsnas.
  3. "Histone H3-K9 methylation potential of Drosophila Su(var)3-9 mutants correlates with extent of gene silencing."
    Schotta G., Ebert A., Lein S., Kubicek S., Krauss V., Jenuwein T., Reuter F.
    Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION TO 509.
  4. "The genome sequence of Drosophila melanogaster."
    Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F., George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N., Sutton G.G., Wortman J.R., Yandell M.D.
    , Zhang Q., Chen L.X., Brandon R.C., Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A., An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E., Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B., Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I., Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C., Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S., Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M., Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M., Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D., Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F., Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D., Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A., Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C., McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C., Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L., Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R., Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V., Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F., Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J., Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R., Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y., Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T., Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S., Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W., Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M., Venter J.C.
    Science 287:2185-2195(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Berkeley.
  5. Cited for: GENOME REANNOTATION.
    Strain: Berkeley.
  6. "Physical and functional association of SU(VAR)3-9 and HDAC1 in Drosophila."
    Czermin B., Schotta G., Huelsmann B.B., Brehm A., Becker P.B., Reuter G., Imhof A.
    EMBO Rep. 2:915-919(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RPD3.
  7. "Central role of Drosophila SU(VAR)3-9 in histone H3-K9 methylation and heterochromatic gene silencing."
    Schotta G., Ebert A., Krauss V., Fischer A., Hoffmann J., Rea S., Jenuwein T., Dorn R., Reuter G.
    EMBO J. 21:1121-1131(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: ENZYME ACTIVITY, INTERACTION WITH SU(VAR)205 AND SU(VAR)3-7.
  8. "Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location."
    Greil F., van der Kraan I., Delrow J., Smothers J.F., de Wit E., Bussemaker H.J., van Driel R., Henikoff S., van Steensel B.
    Genes Dev. 17:2825-2838(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiSUV39_DROME
AccessioniPrimary (citable) accession number: P45975
Secondary accession number(s): Q9VFA6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 21, 2003
Last modified: May 11, 2016
This is version 163 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programDrosophila annotation project

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Drosophila
    Drosophila: entries, gene names and cross-references to FlyBase
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.