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Protein

Histone-lysine N-methyltransferase SETDB2

Gene

setdb2

Organism
Xenopus tropicalis (Western clawed frog) (Silurana tropicalis)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

Histone methyltransferase involved in left-right axis specification in early development and mitosis. Specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). H3K9me3 represents a specific tag for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated histones. Contributes to H3K9me3 in both the interspersed repetitive elements and centromere-associated repeats. Plays a role in chromosome condensation and segregation during mitosis (By similarity).By similarity

Catalytic activityi

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi306Zinc 1By similarity1
Metal bindingi306Zinc 2By similarity1
Metal bindingi308Zinc 1By similarity1
Metal bindingi312Zinc 1By similarity1
Metal bindingi312Zinc 3By similarity1
Metal bindingi318Zinc 1By similarity1
Metal bindingi320Zinc 2By similarity1
Metal bindingi359Zinc 2By similarity1
Metal bindingi359Zinc 3By similarity1
Metal bindingi363Zinc 2By similarity1
Metal bindingi365Zinc 3By similarity1
Metal bindingi370Zinc 3By similarity1
Binding sitei626S-adenosyl-L-methioninePROSITE-ProRule annotation1
Metal bindingi632Zinc 4By similarity1
Metal bindingi685Zinc 4By similarity1
Metal bindingi687Zinc 4By similarity1
Metal bindingi692Zinc 4By similarity1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Developmental protein, Methyltransferase, Transferase

Keywords - Biological processi

Cell cycle, Cell division, Mitosis

Keywords - Ligandi

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

Names & Taxonomyi

Protein namesi
Recommended name:
Histone-lysine N-methyltransferase SETDB2 (EC:2.1.1.43)
Alternative name(s):
SET domain bifurcated 2
Gene namesi
Name:setdb2
OrganismiXenopus tropicalis (Western clawed frog) (Silurana tropicalis)
Taxonomic identifieri8364 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusSilurana
Proteomesi
  • UP000008143 Componenti: Unassembled WGS sequence

Organism-specific databases

XenbaseiXB-GENE-1219030. setdb2.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003986471 – 697Histone-lysine N-methyltransferase SETDB2Add BLAST697

Proteomic databases

PaxDbiA4IGY9.

Interactioni

Protein-protein interaction databases

STRINGi8364.ENSXETP00000034176.

Structurei

3D structure databases

ProteinModelPortaliA4IGY9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini172 – 242MBDPROSITE-ProRule annotationAdd BLAST71
Domaini304 – 378Pre-SETPROSITE-ProRule annotationAdd BLAST75
Domaini381 – 672SETPROSITE-ProRule annotationAdd BLAST292

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni391 – 393S-adenosyl-L-methionine bindingBy similarity3
Regioni629 – 630S-adenosyl-L-methionine bindingBy similarity2

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.PROSITE-ProRule annotation
Contains 1 MBD (methyl-CpG-binding) domain.PROSITE-ProRule annotation
Contains 1 pre-SET domain.PROSITE-ProRule annotation
Contains 1 SET domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG1141. Eukaryota.
ENOG410ZQJZ. LUCA.
HOGENOMiHOG000060314.
HOVERGENiHBG106688.
InParanoidiA4IGY9.
KOiK18494.

Family and domain databases

Gene3Di3.30.890.10. 1 hit.
InterProiIPR016177. DNA-bd_dom.
IPR001739. Methyl_CpG_DNA-bd.
IPR007728. Pre-SET_dom.
IPR001214. SET_dom.
[Graphical view]
PfamiPF01429. MBD. 1 hit.
PF05033. Pre-SET. 1 hit.
PF00856. SET. 1 hit.
[Graphical view]
SMARTiSM00391. MBD. 1 hit.
SM00468. PreSET. 1 hit.
SM00317. SET. 1 hit.
[Graphical view]
SUPFAMiSSF54171. SSF54171. 1 hit.
PROSITEiPS50982. MBD. 1 hit.
PS50867. PRE_SET. 1 hit.
PS50280. SET. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

A4IGY9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MERSTNARHS TLSSWTRESN TLSVLSKDVS LEDAKEYWKD CQADGKVDWI
60 70 80 90 100
FEKLLNKLKI LWQKIKDGSA TNLEYVRAVI LVNEAEQLEE DTETLHTDIQ
110 120 130 140 150
KENKVQENTD CAPERKEDSC ADLNSDCETD VSGSECEHED HSTVSPPATG
160 170 180 190 200
AVCFGKHLCG PSCLSDINPS LLKKENPLNL PVSCDFQRWR VKTNGSEYPP
210 220 230 240 250
HILYKAPCGR SLRDSDEVHS YLTETGCHFL GVDNFSFSTQ VQLESHLSIK
260 270 280 290 300
QEIVQDCDIS NDVESVPVSL SNEIDDTRPT NFIYRKTSWP PGYSINNFTD
310 320 330 340 350
IFVKCCSCTD GCLDISTCSC LQLTAQAFEK FTDSSLGIGP LGYKHKRLQE
360 370 380 390 400
PVPTGLYECN LSCKCDRTLC QNRVVQHGLQ LRLQVFKTDT KGWGVRCLDD
410 420 430 440 450
VDNGTFVCIY AGRILIRTAD SSVKTTLEDS VACGNEAKED NGSTSTLMLS
460 470 480 490 500
KRKRKPSHSD SEVTVMHLTP YSMRSLGLSV HRQSNTLSLT HLRSGGREIS
510 520 530 540 550
LEPFRRPKTK TSMLQKRRRQ LIEEGACTVH NSSEEEGPTP PQSPKQKFNA
560 570 580 590 600
GRKIHRNENS DETASGYVSE ESSSSVISGG HPSEKPTCRT KSKLNKMTPH
610 620 630 640 650
LSTSPEQTCE EDLHFLDASK EGNVGRFLNH SCCPNLFVQH VFVDTHQKSF
660 670 680 690
PWVAFFTNSV VKAGTELTWD YNYVIGTAPD QEIQCLCGQQ TCKHKIV
Length:697
Mass (Da):78,015
Last modified:May 1, 2007 - v1
Checksum:i355475082EA9861D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC135302 mRNA. Translation: AAI35303.1.
RefSeqiNP_001096194.1. NM_001102724.2.
UniGeneiStr.16757.

Genome annotation databases

GeneIDi100124743.
KEGGixtr:100124743.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC135302 mRNA. Translation: AAI35303.1.
RefSeqiNP_001096194.1. NM_001102724.2.
UniGeneiStr.16757.

3D structure databases

ProteinModelPortaliA4IGY9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi8364.ENSXETP00000034176.

Proteomic databases

PaxDbiA4IGY9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi100124743.
KEGGixtr:100124743.

Organism-specific databases

CTDi83852.
XenbaseiXB-GENE-1219030. setdb2.

Phylogenomic databases

eggNOGiKOG1141. Eukaryota.
ENOG410ZQJZ. LUCA.
HOGENOMiHOG000060314.
HOVERGENiHBG106688.
InParanoidiA4IGY9.
KOiK18494.

Family and domain databases

Gene3Di3.30.890.10. 1 hit.
InterProiIPR016177. DNA-bd_dom.
IPR001739. Methyl_CpG_DNA-bd.
IPR007728. Pre-SET_dom.
IPR001214. SET_dom.
[Graphical view]
PfamiPF01429. MBD. 1 hit.
PF05033. Pre-SET. 1 hit.
PF00856. SET. 1 hit.
[Graphical view]
SMARTiSM00391. MBD. 1 hit.
SM00468. PreSET. 1 hit.
SM00317. SET. 1 hit.
[Graphical view]
SUPFAMiSSF54171. SSF54171. 1 hit.
PROSITEiPS50982. MBD. 1 hit.
PS50867. PRE_SET. 1 hit.
PS50280. SET. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSETB2_XENTR
AccessioniPrimary (citable) accession number: A4IGY9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 5, 2010
Last sequence update: May 1, 2007
Last modified: November 30, 2016
This is version 61 of the entry and version 1 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

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.