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Protein

Histone-lysine N-methyltransferase SETDB2

Gene

SETDB2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein 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.1 Publication

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi293 – 2931Zinc 1By similarity
Metal bindingi293 – 2931Zinc 2By similarity
Metal bindingi295 – 2951Zinc 1By similarity
Metal bindingi299 – 2991Zinc 1By similarity
Metal bindingi299 – 2991Zinc 3By similarity
Metal bindingi305 – 3051Zinc 1By similarity
Metal bindingi307 – 3071Zinc 2By similarity
Metal bindingi345 – 3451Zinc 2By similarity
Metal bindingi345 – 3451Zinc 3By similarity
Metal bindingi349 – 3491Zinc 2By similarity
Metal bindingi351 – 3511Zinc 3By similarity
Metal bindingi356 – 3561Zinc 3By similarity
Binding sitei418 – 4181S-adenosyl-L-methioninePROSITE-ProRule annotation
Binding sitei648 – 6481S-adenosyl-L-methioninePROSITE-ProRule annotation
Metal bindingi654 – 6541Zinc 4By similarity
Metal bindingi707 – 7071Zinc 4By similarity
Metal bindingi709 – 7091Zinc 4By similarity
Metal bindingi714 – 7141Zinc 4By similarity

GO - Molecular functioni

GO - Biological processi

  • cell division Source: UniProtKB-KW
  • chromatin organization Source: Reactome
  • chromosome segregation Source: UniProtKB
  • heart looping Source: UniProtKB
  • histone H3-K9 methylation Source: UniProtKB
  • left/right axis specification Source: UniProtKB
  • mitotic nuclear division Source: UniProtKB
  • negative regulation of transcription, DNA-templated Source: UniProtKB
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

Enzyme and pathway databases

ReactomeiREACT_268728. PKMTs methylate histone lysines.

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
Lysine N-methyltransferase 1F
SET domain bifurcated 2
Gene namesi
Name:SETDB2
Synonyms:C13orf4, CLLD8, KMT1F
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 13

Organism-specific databases

HGNCiHGNC:20263. SETDB2.

Subcellular locationi

GO - Cellular componenti

  • chromosome Source: UniProtKB-SubCell
  • nucleoplasm Source: Reactome
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134956285.

Polymorphism and mutation databases

BioMutaiSETDB2.
DMDMi143811459.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 719719Histone-lysine N-methyltransferase SETDB2PRO_0000186088Add
BLAST

Proteomic databases

PaxDbiQ96T68.
PRIDEiQ96T68.

PTM databases

PhosphoSiteiQ96T68.

Expressioni

Tissue specificityi

Ubiquitous. Highest expression in heart, testis and ovary.

Gene expression databases

BgeeiQ96T68.
CleanExiHS_SETDB2.
ExpressionAtlasiQ96T68. baseline and differential.
GenevisibleiQ96T68. HS.

Organism-specific databases

HPAiCAB012190.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
ARL14EPQ8N8R73EBI-1222089,EBI-2807994

Protein-protein interaction databases

BioGridi123768. 3 interactions.
IntActiQ96T68. 2 interactions.
STRINGi9606.ENSP00000326477.

Structurei

3D structure databases

ProteinModelPortaliQ96T68.
SMRiQ96T68. Positions 243-408, 567-715.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini157 – 22973MBDPROSITE-ProRule annotationAdd
BLAST
Domaini291 – 36474Pre-SETPROSITE-ProRule annotationAdd
BLAST
Domaini367 – 694328SETPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni377 – 3793S-adenosyl-L-methionine bindingBy similarity
Regioni651 – 6522S-adenosyl-L-methionine bindingBy similarity

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

eggNOGiCOG2940.
GeneTreeiENSGT00780000121845.
HOVERGENiHBG106688.
InParanoidiQ96T68.
KOiK18494.
OMAiKCHFQRR.
OrthoDBiEOG7ZD1TG.
PhylomeDBiQ96T68.
TreeFamiTF106411.

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]
SMARTiSM00317. SET. 1 hit.
[Graphical view]
SUPFAMiSSF54171. SSF54171. 1 hit.
PROSITEiPS50982. MBD. 1 hit.
PS50867. PRE_SET. 1 hit.
PS50280. SET. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q96T68-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MGEKNGDAKT FWMELEDDGK VDFIFEQVQN VLQSLKQKIK DGSATNKEYI
60 70 80 90 100
QAMILVNEAT IINSSTSIKG ASQKEVNAQS SDPMPVTQKE QENKSNAFPS
110 120 130 140 150
TSCENSFPED CTFLTTENKE ILSLEDKVVD FREKDSSSNL SYQSHDCSGA
160 170 180 190 200
CLMKMPLNLK GENPLQLPIK CHFQRRHAKT NSHSSALHVS YKTPCGRSLR
210 220 230 240 250
NVEEVFRYLL ETECNFLFTD NFSFNTYVQL ARNYPKQKEV VSDVDISNGV
260 270 280 290 300
ESVPISFCNE IDSRKLPQFK YRKTVWPRAY NLTNFSSMFT DSCDCSEGCI
310 320 330 340 350
DITKCACLQL TARNAKTSPL SSDKITTGYK YKRLQRQIPT GIYECSLLCK
360 370 380 390 400
CNRQLCQNRV VQHGPQVRLQ VFKTEQKGWG VRCLDDIDRG TFVCIYSGRL
410 420 430 440 450
LSRANTEKSY GIDENGRDEN TMKNIFSKKR KLEVACSDCE VEVLPLGLET
460 470 480 490 500
HPRTAKTEKC PPKFSNNPKE LTVETKYDNI SRIQYHSVIR DPESKTAIFQ
510 520 530 540 550
HNGKKMEFVS SESVTPEDND GFKPPREHLN SKTKGAQKDS SSNHVDEFED
560 570 580 590 600
NLLIESDVID ITKYREETPP RSRCNQATTL DNQNIKKAIE VQIQKPQEGR
610 620 630 640 650
STACQRQQVF CDEELLSETK NTSSDSLTKF NKGNVFLLDA TKEGNVGRFL
660 670 680 690 700
NHSCCPNLLV QNVFVETHNR NFPLVAFFTN RYVKARTELT WDYGYEAGTV
710
PEKEIFCQCG VNKCRKKIL
Length:719
Mass (Da):81,894
Last modified:April 3, 2007 - v2
Checksum:i01CD2CFE5C1D9067
GO
Isoform 2 (identifier: Q96T68-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     70-81: Missing.

Note: No experimental confirmation available.
Show »
Length:707
Mass (Da):80,707
Checksum:i631679B2687F6FBD
GO
Isoform 3 (identifier: Q96T68-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     523-523: Missing.

Note: No experimental confirmation available.
Show »
Length:718
Mass (Da):81,766
Checksum:iFCBD4B8D5A1A3506
GO

Sequence cautioni

The sequence CAH56265.1 differs from that shown.Contaminating sequence. Potential poly-A sequence.Curated
The sequence CAI10818.2 differs from that shown. Reason: Erroneous gene model prediction. Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti117 – 1171E → G.2 Publications
Corresponds to variant rs7998427 [ dbSNP | Ensembl ].
VAR_031282
Natural varianti473 – 4731V → M.3 Publications
Corresponds to variant rs2057413 [ dbSNP | Ensembl ].
VAR_016976

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei70 – 8112Missing in isoform 2. 1 PublicationVSP_008413Add
BLAST
Alternative sequencei523 – 5231Missing in isoform 3. 1 PublicationVSP_024034

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF334407 mRNA. Translation: AAK38373.1.
AL139321, AL136218 Genomic DNA. Translation: CAH71048.1.
AL136218, AL139321 Genomic DNA. Translation: CAI10817.1.
AL136218 Genomic DNA. Translation: CAI10818.2. Sequence problems.
BC017078 mRNA. Translation: AAH17078.1.
BC047434 mRNA. Translation: AAH47434.1.
AL831937 mRNA. Translation: CAH56265.1. Sequence problems.
CCDSiCCDS53868.1. [Q96T68-2]
CCDS9417.1. [Q96T68-1]
RefSeqiNP_001153780.1. NM_001160308.1. [Q96T68-2]
NP_114121.2. NM_031915.2. [Q96T68-1]
XP_005266625.1. XM_005266568.3. [Q96T68-2]
UniGeneiHs.631789.

Genome annotation databases

EnsembliENST00000317257; ENSP00000326477; ENSG00000136169. [Q96T68-2]
ENST00000354234; ENSP00000346175; ENSG00000136169. [Q96T68-1]
GeneIDi83852.
KEGGihsa:83852.
UCSCiuc001vcz.3. human. [Q96T68-1]
uc001vda.3. human. [Q96T68-2]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF334407 mRNA. Translation: AAK38373.1.
AL139321, AL136218 Genomic DNA. Translation: CAH71048.1.
AL136218, AL139321 Genomic DNA. Translation: CAI10817.1.
AL136218 Genomic DNA. Translation: CAI10818.2. Sequence problems.
BC017078 mRNA. Translation: AAH17078.1.
BC047434 mRNA. Translation: AAH47434.1.
AL831937 mRNA. Translation: CAH56265.1. Sequence problems.
CCDSiCCDS53868.1. [Q96T68-2]
CCDS9417.1. [Q96T68-1]
RefSeqiNP_001153780.1. NM_001160308.1. [Q96T68-2]
NP_114121.2. NM_031915.2. [Q96T68-1]
XP_005266625.1. XM_005266568.3. [Q96T68-2]
UniGeneiHs.631789.

3D structure databases

ProteinModelPortaliQ96T68.
SMRiQ96T68. Positions 243-408, 567-715.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi123768. 3 interactions.
IntActiQ96T68. 2 interactions.
STRINGi9606.ENSP00000326477.

PTM databases

PhosphoSiteiQ96T68.

Polymorphism and mutation databases

BioMutaiSETDB2.
DMDMi143811459.

Proteomic databases

PaxDbiQ96T68.
PRIDEiQ96T68.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000317257; ENSP00000326477; ENSG00000136169. [Q96T68-2]
ENST00000354234; ENSP00000346175; ENSG00000136169. [Q96T68-1]
GeneIDi83852.
KEGGihsa:83852.
UCSCiuc001vcz.3. human. [Q96T68-1]
uc001vda.3. human. [Q96T68-2]

Organism-specific databases

CTDi83852.
GeneCardsiGC13P050018.
H-InvDBHIX0011315.
HGNCiHGNC:20263. SETDB2.
HPAiCAB012190.
MIMi607865. gene.
neXtProtiNX_Q96T68.
PharmGKBiPA134956285.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG2940.
GeneTreeiENSGT00780000121845.
HOVERGENiHBG106688.
InParanoidiQ96T68.
KOiK18494.
OMAiKCHFQRR.
OrthoDBiEOG7ZD1TG.
PhylomeDBiQ96T68.
TreeFamiTF106411.

Enzyme and pathway databases

ReactomeiREACT_268728. PKMTs methylate histone lysines.

Miscellaneous databases

ChiTaRSiSETDB2. human.
GenomeRNAii83852.
NextBioi72831.
PROiQ96T68.
SOURCEiSearch...

Gene expression databases

BgeeiQ96T68.
CleanExiHS_SETDB2.
ExpressionAtlasiQ96T68. baseline and differential.
GenevisibleiQ96T68. HS.

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]
SMARTiSM00317. 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...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and characterization of CLLD6, CLLD7, and CLLD8, novel candidate genes for leukemogenesis at chromosome 13q14, a region commonly deleted in B-cell chronic lymphocytic leukemia."
    Mabuchi H., Fujii H., Calin G., Alder H., Negrini M., Rassenti L., Kipps T.J., Bullrich F., Croce C.M.
    Cancer Res. 61:2870-2877(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), VARIANT GLY-117.
  2. "The DNA sequence and analysis of human chromosome 13."
    Dunham A., Matthews L.H., Burton J., Ashurst J.L., Howe K.L., Ashcroft K.J., Beare D.M., Burford D.C., Hunt S.E., Griffiths-Jones S., Jones M.C., Keenan S.J., Oliver K., Scott C.E., Ainscough R., Almeida J.P., Ambrose K.D., Andrews D.T.
    , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Bannerjee R., Barlow K.F., Bates K., Beasley H., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., Burrill W., Carder C., Carter N.P., Chapman J.C., Clamp M.E., Clark S.Y., Clarke G., Clee C.M., Clegg S.C., Cobley V., Collins J.E., Corby N., Coville G.J., Deloukas P., Dhami P., Dunham I., Dunn M., Earthrowl M.E., Ellington A.G., Faulkner L., Frankish A.G., Frankland J., French L., Garner P., Garnett J., Gilbert J.G.R., Gilson C.J., Ghori J., Grafham D.V., Gribble S.M., Griffiths C., Hall R.E., Hammond S., Harley J.L., Hart E.A., Heath P.D., Howden P.J., Huckle E.J., Hunt P.J., Hunt A.R., Johnson C., Johnson D., Kay M., Kimberley A.M., King A., Laird G.K., Langford C.J., Lawlor S., Leongamornlert D.A., Lloyd D.M., Lloyd C., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., McLaren S.J., McMurray A., Milne S., Moore M.J.F., Nickerson T., Palmer S.A., Pearce A.V., Peck A.I., Pelan S., Phillimore B., Porter K.M., Rice C.M., Searle S., Sehra H.K., Shownkeen R., Skuce C.D., Smith M., Steward C.A., Sycamore N., Tester J., Thomas D.W., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., Whitehead S.L., Willey D.L., Wilming L., Wray P.W., Wright M.W., Young L., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Beck S., Bentley D.R., Rogers J., Ross M.T.
    Nature 428:522-528(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2), VARIANT MET-473.
    Tissue: Colon and Testis.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 332-719 (ISOFORM 3), VARIANT MET-473.
    Tissue: Amygdala.
  5. "CLLD8/KMT1F is a lysine methyltransferase that is important for chromosome segregation."
    Falandry C., Fourel G., Galy V., Ristriani T., Horard B., Bensimon E., Salles G., Gilson E., Magdinier F.
    J. Biol. Chem. 285:20234-20241(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.
  6. Cited for: VARIANTS GLY-117 AND MET-473.

Entry informationi

Entry nameiSETB2_HUMAN
AccessioniPrimary (citable) accession number: Q96T68
Secondary accession number(s): Q5TC65
, Q5TC66, Q5W0A7, Q659A7, Q86UD6, Q96AI6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 3, 2003
Last sequence update: April 3, 2007
Last modified: June 24, 2015
This is version 122 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 13
    Human chromosome 13: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. 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.