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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)DescriptionActionsGraphical viewLength
Metal bindingi412Zinc 1By similarity1
Metal bindingi412Zinc 2By similarity1
Metal bindingi414Zinc 1By similarity1
Metal bindingi421Zinc 1By similarity1
Metal bindingi421Zinc 3By similarity1
Metal bindingi427Zinc 1By similarity1
Metal bindingi428Zinc 1By similarity1
Metal bindingi428Zinc 2By similarity1
Metal bindingi456Zinc 2By similarity1
Metal bindingi456Zinc 3By similarity1
Metal bindingi460Zinc 2By similarity1
Metal bindingi462Zinc 3By similarity1
Metal bindingi466Zinc 3By similarity1
Binding sitei531S-adenosyl-L-methioninePROSITE-ProRule annotation1
Metal bindingi563Zinc 4By similarity1
Metal bindingi623Zinc 4By similarity1
Metal bindingi625Zinc 4By similarity1
Metal bindingi630Zinc 4By similarity1

GO - Molecular functioni

  • 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-427359. SIRT1 negatively regulates rRNA Expression.
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: UniProtKB-SubCell
  • polytene chromosome chromocenter Source: FlyBase
Complete GO annotation...

Keywords - Cellular componenti

Centromere, Chromosome, Nucleus

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL2169720.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001860611 – 635Histone-lysine N-methyltransferase Su(var)3-9Add BLAST635

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

BgeeiFBgn0263755.
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 interactors.
DIPiDIP-23970N.
IntActiP45975. 2 interactors.
MINTiMINT-748988.
STRINGi7227.FBpp0302536.

Chemistry databases

BindingDBiP45975.

Structurei

3D structure databases

ProteinModelPortaliP45975.
SMRiP45975.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini219 – 278ChromoPROSITE-ProRule annotationAdd BLAST60
Domaini410 – 474Pre-SETPROSITE-ProRule annotationAdd BLAST65
Domaini477 – 603SETPROSITE-ProRule annotationAdd BLAST127
Domaini619 – 635Post-SETPROSITE-ProRule annotationAdd BLAST17

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni81 – 188Binds to Su(var)205 and Suvar(3)7Add BLAST108
Regioni488 – 490S-adenosyl-L-methionine bindingBy similarity3
Regioni560 – 561S-adenosyl-L-methionine bindingBy similarity2

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 in 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.
OrthoDBiEOG091G0624.
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)DescriptionActionsGraphical viewLength
Sequence conflicti275T → I in AAF55154 (PubMed:10731132).Curated1
Sequence conflicti509G → E in CAA56376 (PubMed:7915232).Curated1
Sequence conflicti627R → A in AAF55154 (PubMed:10731132).Curated1

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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

Chemistry databases

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.
OrthoDBiEOG091G0624.
PhylomeDBiP45975.

Enzyme and pathway databases

ReactomeiR-DME-427359. SIRT1 negatively regulates rRNA Expression.
SABIO-RKP45975.

Miscellaneous databases

GenomeRNAii41483.
PROiP45975.

Gene expression databases

BgeeiFBgn0263755.
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...

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: November 30, 2016
This is version 169 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.