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Protein

Histone-lysine N-methyltransferase SETDB1

Gene

setdb1

Organism
Xenopus laevis (African clawed frog)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript leveli

Functioni

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 (By similarity).By similarity

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 bindingi755 – 7551Zinc 1By similarity
Metal bindingi755 – 7551Zinc 2By similarity
Metal bindingi757 – 7571Zinc 1By similarity
Metal bindingi761 – 7611Zinc 1By similarity
Metal bindingi761 – 7611Zinc 3By similarity
Metal bindingi767 – 7671Zinc 1By similarity
Metal bindingi769 – 7691Zinc 2By similarity
Metal bindingi807 – 8071Zinc 2By similarity
Metal bindingi807 – 8071Zinc 3By similarity
Metal bindingi811 – 8111Zinc 2By similarity
Metal bindingi813 – 8131Zinc 3By similarity
Metal bindingi818 – 8181Zinc 3By similarity
Binding sitei877 – 8771S-adenosyl-L-methioninePROSITE-ProRule annotation
Binding sitei879 – 8791S-adenosyl-L-methioninePROSITE-ProRule annotation
Binding sitei1198 – 11981S-adenosyl-L-methioninePROSITE-ProRule annotation
Metal bindingi1204 – 12041Zinc 4By similarity
Metal bindingi1257 – 12571Zinc 4By similarity
Metal bindingi1259 – 12591Zinc 4By similarity
Metal bindingi1264 – 12641Zinc 4By similarity

GO - Molecular functioni

  1. DNA binding Source: InterPro
  2. histone-lysine N-methyltransferase activity Source: UniProtKB-EC
  3. zinc ion binding Source: InterPro

GO - Biological processi

  1. regulation of transcription, DNA-templated Source: UniProtKB-KW
  2. 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

Names & Taxonomyi

Protein namesi
Recommended name:
Histone-lysine N-methyltransferase SETDB1 (EC:2.1.1.43)
Alternative name(s):
SET domain bifurcated 1
Gene namesi
Name:setdb1
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

XenbaseiXB-GENE-866480. setdb1.

Subcellular locationi

Nucleus By similarity. Chromosome By similarity
Note: Associated with non-pericentromeric regions of chromatin. Excluded from nucleoli and islands of condensed chromatin (By similarity).By similarity

GO - Cellular componenti

  1. chromosome Source: UniProtKB-SubCell
  2. nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 12691269Histone-lysine N-methyltransferase SETDB1PRO_0000281821Add
BLAST

Structurei

3D structure databases

ProteinModelPortaliQ6INA9.
SMRiQ6INA9. Positions 190-391.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini250 – 31263Tudor 1Add
BLAST
Domaini340 – 39556Tudor 2Add
BLAST
Domaini620 – 69172MBDPROSITE-ProRule annotationAdd
BLAST
Domaini753 – 82674Pre-SETPROSITE-ProRule annotationAdd
BLAST
Domaini829 – 1244416SETPROSITE-ProRule annotationAdd
BLAST
Domaini1253 – 126917Post-SETPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni839 – 8413S-adenosyl-L-methionine bindingBy similarity
Regioni1201 – 12022S-adenosyl-L-methionine bindingBy similarity

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili9 – 6355Sequence AnalysisAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi508 – 58073Gln-richAdd
BLAST

Domaini

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 MBD (methyl-CpG-binding) 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
Contains 2 Tudor domains.Curated

Keywords - Domaini

Coiled coil, Repeat

Phylogenomic databases

HOVERGENiHBG061013.
KOiK11421.

Family and domain databases

InterProiIPR016177. DNA-bd_dom.
IPR025796. Hist-Lys_N-MeTrfase_SETDB1.
IPR001739. Methyl_CpG_DNA-bd.
IPR003616. Post-SET_dom.
IPR007728. Pre-SET_dom.
IPR003606. Pre-SET_Zn-bd_sub.
IPR001214. SET_dom.
IPR002999. Tudor.
[Graphical view]
PfamiPF01429. MBD. 1 hit.
PF05033. Pre-SET. 1 hit.
PF00856. SET. 1 hit.
[Graphical view]
SMARTiSM00391. MBD. 1 hit.
SM00508. PostSET. 1 hit.
SM00468. PreSET. 1 hit.
SM00317. SET. 1 hit.
SM00333. TUDOR. 2 hits.
[Graphical view]
SUPFAMiSSF54171. SSF54171. 1 hit.
PROSITEiPS50982. MBD. 1 hit.
PS50868. POST_SET. 1 hit.
PS50867. PRE_SET. 1 hit.
PS51573. SAM_MT43_SUVAR39_1. 1 hit.
PS50280. SET. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q6INA9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MELEQMVVKE LGISMDDLRE LIDRELEKIE FVKQRKAQLL EMEQLVKQKE
60 70 80 90 100
AEVDHVDKLF DNATRAVDDC ETLVKSLYDQ IGMTYKESSS EDEGSSKPTE
110 120 130 140 150
VIEIPDEDDD DVMSVGSGEA VSKIPKEKHL LREAMAAMKR SRQDVQSIVE
160 170 180 190 200
AIQKKSDGPQ TRFSSHPSSP TSSVGGSNQA SASNDMSKDG DLVVGMRILG
210 220 230 240 250
KKRTKTWHKG TLISIQCVGT GKKFKVKFDN KGKSLLSGNH IAYDYHPPPE
260 270 280 290 300
NLTVGSRVVA KYKDGNQVWL YAGIVAEPPS SKNKMRYLIF FDDGYASYVT
310 320 330 340 350
HAELYPVCRP WSKSWEDIED VSCRDFIQEY VNAYPNRPMV LLKSGQLIKT
360 370 380 390 400
EWEGTWWKSK VEEVDGSLVK ILFLDDKRCE WIYRGSTRLE PMFSMKTSNA
410 420 430 440 450
STQEKQQAGQ QRTRPNVGAI RSKGPVVQFT HDLTGNEPEH NPAAPPSPQS
460 470 480 490 500
MPSPQLIDTD SDSQQAQSKK QVAKKSTSFR PGSAGSGQSS PIPTESVPQP
510 520 530 540 550
PAAPRPFQSN QSVQPVQSIQ PIQPIHNIQT IQTIQGIQTI QAIQPIQSIQ
560 570 580 590 600
TLQPIQTIQP LQTIQTLQGN RIVTSIQQFQ IIRTENIPAE STYKAPKEKL
610 620 630 640 650
FYLPHVCNYT CLSRIRPLSH RGKNPLLVPL LYDFRRMTAR RRVNRKMGFH
660 670 680 690 700
VIYKSPCGLS LRTMPEIERY LFETQCKMLF LEMFCLDPYV LVDRKFQPQK
710 720 730 740 750
PFYYIPDITY GKEDVMLSCV NEIDRTPPPQ VAYSKERIPG KGVFINTGAD
760 770 780 790 800
YLVGCDCTDG CRDKSKCACH QLTIQATACT PGAQSNPMAG YQHKRLEECL
810 820 830 840 850
PTGVYECNKR CKCSANMCNN RLVQHGLQVR LQLFKTQNKG WGIRGLDDIA
860 870 880 890 900
KGSFVCIYAG KILTDDFADK EGLEMGDEYF ANLDHIESVE NFKEGYESDA
910 920 930 940 950
KSSSDSSGVD LKEDHEENSG SEDQEESNDS SDDNFGKNED ITTSSVWRSY
960 970 980 990 1000
ATRRTTRGQK ENGTSETASK DSRTRDETTD CKLPEETSKN KVASWLSSNT
1010 1020 1030 1040 1050
MADSVMDSDS RSSLKMGEAL ETDKPKESEE ASKYPRFAEG NRAYGYNPTP
1060 1070 1080 1090 1100
TKKDGVRRPV TKTALHQIKR QSSSAQPTEE VLTLSSSSDS EVGSGTNGSK
1110 1120 1130 1140 1150
KPAAQATAND SDDIQTISSG SDEEEEKKNV AASAGPVKRQ VAVKSTRGFA
1160 1170 1180 1190 1200
LKSTHGITVK SNMASGEGGP GRRNTRQFFD GEESCYIIDA KLEGNLGRYL
1210 1220 1230 1240 1250
NHSCSPNLFV QNVFVDTHDL RFPWVAFFAS KRIRAGTELT WDYNYEVGSV
1260
EGKKLLCCCG STECRGRLL
Length:1,269
Mass (Da):141,777
Last modified:July 4, 2004 - v1
Checksum:i6241910CB4266FAC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC072374 mRNA. Translation: AAH72374.1.
RefSeqiNP_001085076.2. NM_001091607.1.
UniGeneiXl.54988.

Genome annotation databases

GeneIDi432147.
KEGGixla:432147.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC072374 mRNA. Translation: AAH72374.1.
RefSeqiNP_001085076.2. NM_001091607.1.
UniGeneiXl.54988.

3D structure databases

ProteinModelPortaliQ6INA9.
SMRiQ6INA9. Positions 190-391.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi432147.
KEGGixla:432147.

Organism-specific databases

CTDi9869.
XenbaseiXB-GENE-866480. setdb1.

Phylogenomic databases

HOVERGENiHBG061013.
KOiK11421.

Family and domain databases

InterProiIPR016177. DNA-bd_dom.
IPR025796. Hist-Lys_N-MeTrfase_SETDB1.
IPR001739. Methyl_CpG_DNA-bd.
IPR003616. Post-SET_dom.
IPR007728. Pre-SET_dom.
IPR003606. Pre-SET_Zn-bd_sub.
IPR001214. SET_dom.
IPR002999. Tudor.
[Graphical view]
PfamiPF01429. MBD. 1 hit.
PF05033. Pre-SET. 1 hit.
PF00856. SET. 1 hit.
[Graphical view]
SMARTiSM00391. MBD. 1 hit.
SM00508. PostSET. 1 hit.
SM00468. PreSET. 1 hit.
SM00317. SET. 1 hit.
SM00333. TUDOR. 2 hits.
[Graphical view]
SUPFAMiSSF54171. SSF54171. 1 hit.
PROSITEiPS50982. MBD. 1 hit.
PS50868. POST_SET. 1 hit.
PS50867. PRE_SET. 1 hit.
PS51573. SAM_MT43_SUVAR39_1. 1 hit.
PS50280. SET. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. NIH - Xenopus Gene Collection (XGC) project
    Submitted (MAY-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Oocyte.

Entry informationi

Entry nameiSETB1_XENLA
AccessioniPrimary (citable) accession number: Q6INA9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 2, 2007
Last sequence update: July 4, 2004
Last modified: January 6, 2015
This is version 75 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

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.