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Q96T68

- SETB2_HUMAN

UniProt

Q96T68 - SETB2_HUMAN

Protein

Histone-lysine N-methyltransferase SETDB2

Gene

SETDB2

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 113 (01 Oct 2014)
      Sequence version 2 (03 Apr 2007)
      Previous versions | rss
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    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

    1. DNA binding Source: InterPro
    2. histone methyltransferase activity (H3-K9 specific) Source: UniProtKB
    3. zinc ion binding Source: InterPro

    GO - Biological processi

    1. chromosome segregation Source: UniProtKB
    2. heart looping Source: UniProtKB
    3. histone H3-K9 methylation Source: UniProtKB
    4. left/right axis specification Source: UniProtKB
    5. mitotic nuclear division Source: UniProtKB
    6. negative regulation of transcription, DNA-templated Source: UniProtKB

    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
    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: Chromosome 13

    Organism-specific databases

    HGNCiHGNC:20263. SETDB2.

    Subcellular locationi

    Nucleus 1 Publication. Chromosome 1 Publication

    GO - Cellular componenti

    1. chromosome Source: UniProtKB-SubCell
    2. nucleus Source: UniProtKB

    Keywords - Cellular componenti

    Chromosome, Nucleus

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA134956285.

    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

    ArrayExpressiQ96T68.
    BgeeiQ96T68.
    CleanExiHS_SETDB2.
    GenevestigatoriQ96T68.

    Organism-specific databases

    HPAiCAB012190.

    Interactioni

    Protein-protein interaction databases

    BioGridi123768. 2 interactions.
    IntActiQ96T68. 1 interaction.
    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.
    HOVERGENiHBG106688.
    InParanoidiQ96T68.
    KOiK11421.
    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. Align

    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

    MGEKNGDAKT FWMELEDDGK VDFIFEQVQN VLQSLKQKIK DGSATNKEYI    50
    QAMILVNEAT IINSSTSIKG ASQKEVNAQS SDPMPVTQKE QENKSNAFPS 100
    TSCENSFPED CTFLTTENKE ILSLEDKVVD FREKDSSSNL SYQSHDCSGA 150
    CLMKMPLNLK GENPLQLPIK CHFQRRHAKT NSHSSALHVS YKTPCGRSLR 200
    NVEEVFRYLL ETECNFLFTD NFSFNTYVQL ARNYPKQKEV VSDVDISNGV 250
    ESVPISFCNE IDSRKLPQFK YRKTVWPRAY NLTNFSSMFT DSCDCSEGCI 300
    DITKCACLQL TARNAKTSPL SSDKITTGYK YKRLQRQIPT GIYECSLLCK 350
    CNRQLCQNRV VQHGPQVRLQ VFKTEQKGWG VRCLDDIDRG TFVCIYSGRL 400
    LSRANTEKSY GIDENGRDEN TMKNIFSKKR KLEVACSDCE VEVLPLGLET 450
    HPRTAKTEKC PPKFSNNPKE LTVETKYDNI SRIQYHSVIR DPESKTAIFQ 500
    HNGKKMEFVS SESVTPEDND GFKPPREHLN SKTKGAQKDS SSNHVDEFED 550
    NLLIESDVID ITKYREETPP RSRCNQATTL DNQNIKKAIE VQIQKPQEGR 600
    STACQRQQVF CDEELLSETK NTSSDSLTKF NKGNVFLLDA TKEGNVGRFL 650
    NHSCCPNLLV QNVFVETHNR NFPLVAFFTN RYVKARTELT WDYGYEAGTV 700
    PEKEIFCQCG VNKCRKKIL 719
    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. Reason: Contaminating sequence. Potential poly-A sequence.
    The sequence CAI10818.2 differs from that shown. Reason: Erroneous gene model prediction.

    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:
    EMBL
    GenBank
    DDBJ
    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_005266568.2. [Q96T68-2]
    UniGeneiHs.631789.

    Genome annotation databases

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

    Polymorphism databases

    DMDMi143811459.

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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.
    CCDSi CCDS53868.1. [Q96T68-2 ]
    CCDS9417.1. [Q96T68-1 ]
    RefSeqi NP_001153780.1. NM_001160308.1. [Q96T68-2 ]
    NP_114121.2. NM_031915.2. [Q96T68-1 ]
    XP_005266625.1. XM_005266568.2. [Q96T68-2 ]
    UniGenei Hs.631789.

    3D structure databases

    ProteinModelPortali Q96T68.
    SMRi Q96T68. Positions 243-408, 567-715.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 123768. 2 interactions.
    IntActi Q96T68. 1 interaction.
    STRINGi 9606.ENSP00000326477.

    PTM databases

    PhosphoSitei Q96T68.

    Polymorphism databases

    DMDMi 143811459.

    Proteomic databases

    PaxDbi Q96T68.
    PRIDEi Q96T68.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000317257 ; ENSP00000326477 ; ENSG00000136169 . [Q96T68-1 ]
    ENST00000354234 ; ENSP00000346175 ; ENSG00000136169 . [Q96T68-2 ]
    GeneIDi 83852.
    KEGGi hsa:83852.
    UCSCi uc001vcz.3. human. [Q96T68-1 ]
    uc001vda.3. human. [Q96T68-2 ]

    Organism-specific databases

    CTDi 83852.
    GeneCardsi GC13P050018.
    H-InvDB HIX0011315.
    HGNCi HGNC:20263. SETDB2.
    HPAi CAB012190.
    MIMi 607865. gene.
    neXtProti NX_Q96T68.
    PharmGKBi PA134956285.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG2940.
    HOVERGENi HBG106688.
    InParanoidi Q96T68.
    KOi K11421.
    OMAi KCHFQRR.
    OrthoDBi EOG7ZD1TG.
    PhylomeDBi Q96T68.
    TreeFami TF106411.

    Miscellaneous databases

    GenomeRNAii 83852.
    NextBioi 72831.
    PROi Q96T68.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q96T68.
    Bgeei Q96T68.
    CleanExi HS_SETDB2.
    Genevestigatori Q96T68.

    Family and domain databases

    Gene3Di 3.30.890.10. 1 hit.
    InterProi IPR016177. DNA-bd_dom.
    IPR001739. Methyl_CpG_DNA-bd.
    IPR007728. Pre-SET_dom.
    IPR001214. SET_dom.
    [Graphical view ]
    Pfami PF01429. MBD. 1 hit.
    PF05033. Pre-SET. 1 hit.
    PF00856. SET. 1 hit.
    [Graphical view ]
    SMARTi SM00317. SET. 1 hit.
    [Graphical view ]
    SUPFAMi SSF54171. SSF54171. 1 hit.
    PROSITEi PS50982. MBD. 1 hit.
    PS50867. PRE_SET. 1 hit.
    PS50280. SET. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 113 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