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Protein

Histone-lysine N-methyltransferase SETDB2

Gene

setdb2

Organism
Xenopus laevis (African clawed frog)
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 is a specific tag for epigenetic transcriptional repression that recruits 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 bindingi312Zinc 1By similarity1
Metal bindingi312Zinc 2By similarity1
Metal bindingi314Zinc 1By similarity1
Metal bindingi318Zinc 1By similarity1
Metal bindingi318Zinc 3By similarity1
Metal bindingi324Zinc 1By similarity1
Metal bindingi326Zinc 2By similarity1
Metal bindingi365Zinc 2By similarity1
Metal bindingi365Zinc 3By similarity1
Metal bindingi369Zinc 2By similarity1
Metal bindingi371Zinc 3By similarity1
Metal bindingi376Zinc 3By similarity1
Binding sitei632S-adenosyl-L-methioninePROSITE-ProRule annotation1
Metal bindingi638Zinc 4By similarity1
Metal bindingi691Zinc 4By similarity1
Metal bindingi693Zinc 4By similarity1
Metal bindingi698Zinc 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):
Chronic lymphocytic leukemia deletion region gene 8 protein homolog
SET domain bifurcated 2
Gene namesi
Name:setdb2
Synonyms:clld8
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

XenbaseiXB-GENE-1219036. setdb2.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002818251 – 703Histone-lysine N-methyltransferase SETDB2Add BLAST703

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini178 – 248MBDAdd BLAST71
Domaini310 – 384Pre-SETPROSITE-ProRule annotationAdd BLAST75
Domaini387 – 678SETPROSITE-ProRule annotationAdd BLAST292

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni397 – 399S-adenosyl-L-methionine bindingBy similarity3
Regioni635 – 636S-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 pre-SET domain.PROSITE-ProRule annotation
Contains 1 SET domain.PROSITE-ProRule annotation

Phylogenomic databases

HOVERGENiHBG106688.
KOiK18494.

Family and domain databases

Gene3Di3.30.890.10. 1 hit.
InterProiIPR016177. DNA-bd_dom.
IPR001739. Methyl_CpG_DNA-bd.
IPR003616. Post-SET_dom.
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.
PROSITEiPS50868. POST_SET. 1 hit.
PS50867. PRE_SET. 1 hit.
PS50280. SET. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q6YI93-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEQSANARQS TLRSRTQELN TLSVLSKDVS LEDAKKYWKD RQADGKVDWI
60 70 80 90 100
FEKVLNKLKI LWQKIKDGSA TNLEYVRAVI LVNEAGNLEE DLEEDLKEDT
110 120 130 140 150
DTIHIDIHKE NEVQENTDCS PERKEDTCLN LNTDCGTDVS GSEPECNSTV
160 170 180 190 200
SPPAAERVYF GNHSCGPSCL SGINSFLFTK GNPLQLPISC DFQRCHLKIN
210 220 230 240 250
SPDDLSHILY KAPCGRSLRD YDEVHSYLTE TGCHFLAVDN FSFNNHVRLD
260 270 280 290 300
SNSSFNQGIV QDCDISNDVE SVPVAFSNEI DNTRPSNFIY RKTSWPPGYS
310 320 330 340 350
LNNFTDIFVK CCNCTDGCLD ILTCSCLQLT AQAFTKCMES SLGIGPLGYK
360 370 380 390 400
HKRLQEPIPT GLYECNVSCK CDRMLCQNRV VQHGLKLRLQ VFKTNTKGWG
410 420 430 440 450
VRCLDDVDKG TFVCIYAGRI LIRTADCTVK STPDDSVACG NEDHEDSTST
460 470 480 490 500
CALILSKRKR KTSHSDSEVT VMHTNPYSMR SHGLSVHRLS NTFSPRQARS
510 520 530 540 550
GEREFSLQPL RRPKTKTSML QKRRRQLIEE GACTVQNSSE EEGPTPPQSP
560 570 580 590 600
EQKSSAGTKI QRNENSDETA SGYVSEESSS SVISGGHPLE KPISKFKSKL
610 620 630 640 650
NKTTVYLSTS PEQTCEENLH FLDASKEGNV GRFLNHSCCP NLFVQQVFVD
660 670 680 690 700
THQKCFPWVA FFTNSVVKAG TELTWDYSYD IGTAADQEIQ CLCGQKTCKN

KVV
Length:703
Mass (Da):78,698
Last modified:October 5, 2010 - v2
Checksum:i12D86C32892B5325
GO

Sequence cautioni

The sequence AAN61106 differs from that shown. Reason: Frameshift at position 695.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti97K → Q in AAN61106 (Ref. 1) Curated1
Sequence conflicti175S → P in AAN61106 (Ref. 1) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY145835 mRNA. Translation: AAN61106.1. Frameshift.
BC170303 mRNA. Translation: AAI70303.1.
RefSeqiNP_001082765.1. NM_001089296.1.
UniGeneiXl.29790.

Genome annotation databases

GeneIDi398711.
KEGGixla:398711.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY145835 mRNA. Translation: AAN61106.1. Frameshift.
BC170303 mRNA. Translation: AAI70303.1.
RefSeqiNP_001082765.1. NM_001089296.1.
UniGeneiXl.29790.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi398711.
KEGGixla:398711.

Organism-specific databases

CTDi83852.
XenbaseiXB-GENE-1219036. setdb2.

Phylogenomic databases

HOVERGENiHBG106688.
KOiK18494.

Family and domain databases

Gene3Di3.30.890.10. 1 hit.
InterProiIPR016177. DNA-bd_dom.
IPR001739. Methyl_CpG_DNA-bd.
IPR003616. Post-SET_dom.
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.
PROSITEiPS50868. POST_SET. 1 hit.
PS50867. PRE_SET. 1 hit.
PS50280. SET. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSETB2_XENLA
AccessioniPrimary (citable) accession number: Q6YI93
Secondary accession number(s): B7ZRV6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: October 5, 2010
Last modified: November 30, 2016
This is version 70 of the entry and version 2 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

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.