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Protein

Histone-lysine N-methyltransferase SUV39H1-A

Gene

suv39h1a

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript 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 HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated histones. Mainly functions in heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin at pericentric and telomere regions. H3 'Lys-9' trimethylation is also required to direct DNA methylation at pericentric repeats. SUV39H1 is targeted to histone H3 via its interaction with RB1 and is involved in many processes, such as regulation of organ-specific terminal differentiation during development.1 Publication

Catalytic activityi

S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].PROSITE-ProRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi180 – 1801Zinc 1By similarity
Metal bindingi180 – 1801Zinc 2By similarity
Metal bindingi182 – 1821Zinc 1By similarity
Metal bindingi185 – 1851Zinc 1By similarity
Metal bindingi185 – 1851Zinc 3By similarity
Metal bindingi193 – 1931Zinc 1By similarity
Metal bindingi194 – 1941Zinc 1By similarity
Metal bindingi194 – 1941Zinc 2By similarity
Metal bindingi221 – 2211Zinc 2By similarity
Metal bindingi221 – 2211Zinc 3By similarity
Metal bindingi225 – 2251Zinc 2By similarity
Metal bindingi227 – 2271Zinc 3By similarity
Metal bindingi231 – 2311Zinc 3By similarity
Binding sitei296 – 2961S-adenosyl-L-methioninePROSITE-ProRule annotation
Metal bindingi325 – 3251Zinc 4By similarity
Metal bindingi399 – 3991Zinc 4By similarity
Metal bindingi401 – 4011Zinc 4By similarity
Metal bindingi406 – 4061Zinc 4By similarity

GO - Molecular functioni

GO - Biological processi

  • cell cycle Source: UniProtKB-KW
  • cell differentiation Source: UniProtKB-KW
  • exocrine pancreas development Source: ZFIN
  • histone H3-K9 methylation Source: ZFIN
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • retina morphogenesis in camera-type eye Source: ZFIN
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Methyltransferase, Repressor, Transferase

Keywords - Biological processi

Cell cycle, Differentiation, Transcription, Transcription regulation

Keywords - Ligandi

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

Enzyme and pathway databases

ReactomeiREACT_294904. PKMTs methylate histone lysines.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone-lysine N-methyltransferase SUV39H1-A (EC:2.1.1.43)
Alternative name(s):
Suppressor of variegation 3-9 homolog 1-A
Short name:
Su(var)3-9 homolog 1-A
Gene namesi
Name:suv39h1a
Synonyms:suv39h1
ORF Names:si:dkey-16n15.2, zgc:101027
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
ProteomesiUP000000437 Componenti: Chromosome 8

Organism-specific databases

ZFINiZDB-GENE-040801-111. suv39h1a.

Subcellular locationi

  • Nucleus By similarity
  • Chromosomecentromere By similarity

  • Note: Associates with centromeric constitutive heterochromatin.By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Centromere, Chromosome, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 411411Histone-lysine N-methyltransferase SUV39H1-APRO_0000281811Add
BLAST

Expressioni

Tissue specificityi

Expressed ubuitiously.1 Publication

Developmental stagei

Expressed both maternally and zygotically.1 Publication

Gene expression databases

BgeeiQ6DGD3.

Interactioni

Protein-protein interaction databases

STRINGi7955.ENSDARP00000034818.

Structurei

3D structure databases

ProteinModelPortaliQ6DGD3.
SMRiQ6DGD3. Positions 115-410.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini43 – 10159ChromoPROSITE-ProRule annotationAdd
BLAST
Domaini178 – 23962Pre-SETPROSITE-ProRule annotationAdd
BLAST
Domaini242 – 365124SETPROSITE-ProRule annotationAdd
BLAST
Domaini395 – 41117Post-SETPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni253 – 2553S-adenosyl-L-methionine bindingBy similarity
Regioni322 – 3232S-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

eggNOGiCOG2940.
GeneTreeiENSGT00780000121845.
HOGENOMiHOG000231244.
HOVERGENiHBG055621.
InParanoidiQ6DGD3.
KOiK11419.
OMAiWVKMATH.
OrthoDBiEOG7RJPR0.
PhylomeDBiQ6DGD3.
TreeFamiTF106452.

Family and domain databases

InterProiIPR000953. Chromo/shadow_dom.
IPR023780. Chromo_domain.
IPR016197. Chromodomain-like.
IPR023779. Chromodomain_CS.
IPR011381. Histone_H3-K9_MeTrfase.
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.
SM00508. PostSET. 1 hit.
SM00317. SET. 1 hit.
[Graphical view]
SUPFAMiSSF54160. SSF54160. 1 hit.
PROSITEiPS00598. CHROMO_1. 1 hit.
PS50013. CHROMO_2. 1 hit.
PS50868. POST_SET. 1 hit.
PS50867. PRE_SET. 1 hit.
PS51579. SAM_MT43_SUVAR39_3. 1 hit.
PS50280. SET. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q6DGD3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MARDLKDCRV PCKLLLEDLQ ALCRRKKLVC KQLSVTKNNF NDYEVEYLCN
60 70 80 90 100
YKKHKGREFF LVKWKGYEES ENTWEPLKNL KCPILLHQFR KDMKAALLQA
110 120 130 140 150
NEPLDSASLS GPIISFLRQK ATQRIRLKKW EDLMNQTCWH KGRIFVSNEV
160 170 180 190 200
DMDGPPKNFT YINENKLGKG VDMNAVIVGC ECEDCVSQPV DGCCPGLLKF
210 220 230 240 250
RRAYNESRRV KVMPGVPIYE CNSKCRCGPD CANRVVQRGI QYDLCIFKTD
260 270 280 290 300
NGRGWGVRTL QRINKNSFVM EYLGEIITTD EAEQRGVLYD KQGVTYLFDL
310 320 330 340 350
DYVDDVYTID AAHYGNISHF VNHSCDPNLQ VYNVFIDNLD ERLPRIALFA
360 370 380 390 400
KRGIKAGEEL TFDYKMTVDP VDAESTKMDL DFSRAGIEGS PIKRVHMECK
410
CGVRNCRKYL F
Length:411
Mass (Da):47,471
Last modified:October 14, 2008 - v2
Checksum:i3C86D47CEC18C150
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti139 – 1391W → R in AAH76417 (Ref. 2) Curated
Sequence conflicti152 – 1521M → L in AAH76417 (Ref. 2) Curated
Sequence conflicti183 – 1831E → A in AAH76417 (Ref. 2) Curated
Sequence conflicti284 – 2841Q → R in AAH76417 (Ref. 2) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX005340 Genomic DNA. Translation: CAQ14784.1.
BC076417 mRNA. Translation: AAH76417.1.
DQ840140 mRNA. Translation: ABI34869.1.
RefSeqiNP_001003592.1. NM_001003592.1.
UniGeneiDr.80633.

Genome annotation databases

EnsembliENSDART00000038955; ENSDARP00000034818; ENSDARG00000026799.
GeneIDi445198.
KEGGidre:445198.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX005340 Genomic DNA. Translation: CAQ14784.1.
BC076417 mRNA. Translation: AAH76417.1.
DQ840140 mRNA. Translation: ABI34869.1.
RefSeqiNP_001003592.1. NM_001003592.1.
UniGeneiDr.80633.

3D structure databases

ProteinModelPortaliQ6DGD3.
SMRiQ6DGD3. Positions 115-410.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000034818.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSDART00000038955; ENSDARP00000034818; ENSDARG00000026799.
GeneIDi445198.
KEGGidre:445198.

Organism-specific databases

CTDi445198.
ZFINiZDB-GENE-040801-111. suv39h1a.

Phylogenomic databases

eggNOGiCOG2940.
GeneTreeiENSGT00780000121845.
HOGENOMiHOG000231244.
HOVERGENiHBG055621.
InParanoidiQ6DGD3.
KOiK11419.
OMAiWVKMATH.
OrthoDBiEOG7RJPR0.
PhylomeDBiQ6DGD3.
TreeFamiTF106452.

Enzyme and pathway databases

ReactomeiREACT_294904. PKMTs methylate histone lysines.

Miscellaneous databases

NextBioi20831958.
PROiQ6DGD3.

Gene expression databases

BgeeiQ6DGD3.

Family and domain databases

InterProiIPR000953. Chromo/shadow_dom.
IPR023780. Chromo_domain.
IPR016197. Chromodomain-like.
IPR023779. Chromodomain_CS.
IPR011381. Histone_H3-K9_MeTrfase.
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.
SM00508. PostSET. 1 hit.
SM00317. SET. 1 hit.
[Graphical view]
SUPFAMiSSF54160. SSF54160. 1 hit.
PROSITEiPS00598. CHROMO_1. 1 hit.
PS50013. CHROMO_2. 1 hit.
PS50868. POST_SET. 1 hit.
PS50867. PRE_SET. 1 hit.
PS51579. SAM_MT43_SUVAR39_3. 1 hit.
PS50280. SET. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The zebrafish reference genome sequence and its relationship to the human genome."
    Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.
    , White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M., Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J., Clee C., Oliver K., Clark R., Riddle C., Eliott D., Threadgold G., Harden G., Ware D., Mortimer B., Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M., Rudolph-Geiger S., Teucke M., Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.
    Nature 496:498-503(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Tuebingen.
  2. NIH - Zebrafish Gene Collection (ZGC) project
    Submitted (JUL-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Embryo.
  3. "Genome-wide survey and developmental expression mapping of zebrafish SET domain-containing genes."
    Sun X.-J., Xu P.-F., Zhou T., Hu M., Fu C.-T., Zhang Y., Jin Y., Chen Y., Chen S.-J., Huang Q.-H., Liu T.X., Chen Z.
    PLoS ONE 3:E1499-E1499(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 214-409, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
  4. "Zebra fish Dnmt1 and Suv39h1 regulate organ-specific terminal differentiation during development."
    Rai K., Nadauld L.D., Chidester S., Manos E.J., James S.R., Karpf A.R., Cairns B.R., Jones D.A.
    Mol. Cell. Biol. 26:7077-7085(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiSV91A_DANRE
AccessioniPrimary (citable) accession number: Q6DGD3
Secondary accession number(s): A5XBP4, B0S580
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: October 14, 2008
Last modified: June 24, 2015
This is version 87 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.