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Q9UJW3

- DNM3L_HUMAN

UniProt

Q9UJW3 - DNM3L_HUMAN

Protein

DNA (cytosine-5)-methyltransferase 3-like

Gene

DNMT3L

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 119 (01 Oct 2014)
      Sequence version 3 (31 May 2011)
      Previous versions | rss
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    Functioni

    Catalytically inactive regulatory factor of DNA methyltransferases. It is essential for the function of DNMT3A and DNMT3B. Activates DNMT3A and DNMT3B by binding to their catalytic domain. Accelerates the binding of DNA and AdoMet to the methyltransferases and dissociates from the complex after DNA binding to the methyltransferases. Recognizes unmethylated histone H3 lysine 4 (H3K4) and induces de novo DNA methylation by recruitment or activation of DNMT3.1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri52 – 8231GATA-type; atypicalPROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri93 – 14957PHD-type; atypicalPROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. enzyme activator activity Source: MGI
    2. enzyme binding Source: UniProtKB
    3. metal ion binding Source: UniProtKB-KW
    4. protein binding Source: UniProtKB

    GO - Biological processi

    1. chorionic trophoblast cell differentiation Source: Ensembl
    2. DNA methylation Source: UniProtKB
    3. in utero embryonic development Source: Ensembl
    4. negative regulation of transcription, DNA-templated Source: UniProtKB
    5. placenta development Source: Ensembl
    6. regulation of gene expression by genetic imprinting Source: UniProtKB
    7. spermatogenesis Source: UniProtKB

    Keywords - Ligandi

    Metal-binding, Zinc

    Protein family/group databases

    REBASEi4636. M.HsaDnmt3L.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA (cytosine-5)-methyltransferase 3-like
    Gene namesi
    Name:DNMT3L
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 21

    Organism-specific databases

    HGNCiHGNC:2980. DNMT3L.

    Subcellular locationi

    Nucleus Curated

    GO - Cellular componenti

    1. condensed nuclear chromosome Source: Ensembl
    2. cytosol Source: UniProtKB
    3. nuclear heterochromatin Source: Ensembl
    4. nucleus Source: UniProtKB

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi261 – 2611F → A: Loss of binding to DNMT3A. 1 Publication

    Organism-specific databases

    PharmGKBiPA27447.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 386386DNA (cytosine-5)-methyltransferase 3-likePRO_0000088047Add
    BLAST

    Proteomic databases

    PaxDbiQ9UJW3.
    PRIDEiQ9UJW3.

    PTM databases

    PhosphoSiteiQ9UJW3.

    Expressioni

    Tissue specificityi

    Expressed at low levels in several tissues including testis, ovary, and thymus.

    Gene expression databases

    ArrayExpressiQ9UJW3.
    BgeeiQ9UJW3.
    CleanExiHS_DNMT3L.
    GenevestigatoriQ9UJW3.

    Interactioni

    Subunit structurei

    Homodimer. Heterotetramer composed of 1 DNMT3A homodimer and 2 DNMT3L subunits (DNMT3L-DNMT3A-DNMT3A-DNMT3L). Interacts with histone H3 (via N-terminus).1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    HDAC1Q135473EBI-740967,EBI-301834

    Protein-protein interaction databases

    BioGridi118984. 11 interactions.
    DIPiDIP-35238N.
    IntActiQ9UJW3. 7 interactions.
    MINTiMINT-1448248.
    STRINGi9606.ENSP00000270172.

    Structurei

    Secondary structure

    1
    386
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi35 – 439
    Helixi49 – 513
    Turni54 – 563
    Beta strandi66 – 716
    Helixi74 – 818
    Turni82 – 854
    Beta strandi89 – 935
    Turni97 – 993
    Helixi119 – 1257
    Helixi130 – 1367
    Turni143 – 1453
    Beta strandi154 – 1563
    Helixi160 – 17112
    Helixi184 – 1863
    Beta strandi192 – 1976
    Turni200 – 2078
    Beta strandi218 – 2225
    Helixi229 – 2346
    Beta strandi239 – 2446
    Turni248 – 2503
    Helixi257 – 27014
    Beta strandi281 – 2866
    Helixi292 – 30211
    Beta strandi308 – 3103
    Beta strandi314 – 3163
    Beta strandi322 – 3254
    Beta strandi327 – 3315
    Helixi340 – 35112
    Helixi362 – 3654
    Helixi369 – 3735

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2PV0X-ray3.30A/B/C1-386[»]
    2PVCX-ray3.69A/B/C1-386[»]
    2QRVX-ray2.89B/C/F/G160-386[»]
    ProteinModelPortaliQ9UJW3.
    SMRiQ9UJW3. Positions 34-380.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9UJW3.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini41 – 173133ADDPROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Contains 1 ADD domain.PROSITE-ProRule annotation
    Contains 1 GATA-type zinc finger.PROSITE-ProRule annotation
    Contains 1 PHD-type zinc finger.PROSITE-ProRule annotation

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri52 – 8231GATA-type; atypicalPROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri93 – 14957PHD-type; atypicalPROSITE-ProRule annotationAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiNOG69419.
    HOGENOMiHOG000246422.
    HOVERGENiHBG051382.
    InParanoidiQ9UJW3.
    KOiK17400.
    OMAiTVPVWKR.
    TreeFamiTF329039.

    Family and domain databases

    Gene3Di3.30.40.10. 1 hit.
    InterProiIPR025766. ADD.
    IPR011011. Znf_FYVE_PHD.
    IPR013083. Znf_RING/FYVE/PHD.
    [Graphical view]
    SUPFAMiSSF57903. SSF57903. 1 hit.
    PROSITEiPS51533. ADD. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Note: Other splice isoforms seem to exist.

    Isoform 1 (identifier: Q9UJW3-1) [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

    MAAIPALDPE AEPSMDVILV GSSELSSSVS PGTGRDLIAY EVKANQRNIE    50
    DICICCGSLQ VHTQHPLFEG GICAPCKDKF LDALFLYDDD GYQSYCSICC 100
    SGETLLICGN PDCTRCYCFE CVDSLVGPGT SGKVHAMSNW VCYLCLPSSR 150
    SGLLQRRRKW RSQLKAFYDR ESENPLEMFE TVPVWRRQPV RVLSLFEDIK 200
    KELTSLGFLE SGSDPGQLKH VVDVTDTVRK DVEEWGPFDL VYGATPPLGH 250
    TCDRPPSWYL FQFHRLLQYA RPKPGSPRPF FWMFVDNLVL NKEDLDVASR 300
    FLEMEPVTIP DVHGGSLQNA VRVWSNIPAI RSRHWALVSE EELSLLAQNK 350
    QSSKLAAKWP TKLVKNCFLP LREYFKYFST ELTSSL 386
    Length:386
    Mass (Da):43,583
    Last modified:May 31, 2011 - v3
    Checksum:i65EC2AB7492D53B3
    GO
    Isoform 2 (identifier: Q9UJW3-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         332-332: S → SS

    Show »
    Length:387
    Mass (Da):43,670
    Checksum:i699AAC1929D473A9
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti246 – 2461P → A in AAF05812. (PubMed:10857753)Curated
    Sequence conflicti266 – 2661L → F in AAF05812. (PubMed:10857753)Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti278 – 2781R → G.1 Publication
    Corresponds to variant rs7354779 [ dbSNP | Ensembl ].
    VAR_051962

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei332 – 3321S → SS in isoform 2. 1 PublicationVSP_041295

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF194032 mRNA. Translation: AAF05812.1.
    AP001753 Genomic DNA. Translation: BAA95556.1.
    AP001059 Genomic DNA. No translation available.
    AP001060 Genomic DNA. No translation available.
    CH471079 Genomic DNA. Translation: EAX09445.1.
    BC002560 mRNA. Translation: AAH02560.1.
    CCDSiCCDS13705.1. [Q9UJW3-2]
    CCDS46650.1. [Q9UJW3-1]
    RefSeqiNP_037501.2. NM_013369.3. [Q9UJW3-2]
    NP_787063.1. NM_175867.2. [Q9UJW3-1]
    UniGeneiHs.592165.

    Genome annotation databases

    EnsembliENST00000270172; ENSP00000270172; ENSG00000142182. [Q9UJW3-2]
    GeneIDi29947.
    KEGGihsa:29947.
    UCSCiuc002zeg.2. human. [Q9UJW3-1]
    uc002zeh.2. human. [Q9UJW3-2]

    Polymorphism databases

    DMDMi334302913.

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF194032 mRNA. Translation: AAF05812.1 .
    AP001753 Genomic DNA. Translation: BAA95556.1 .
    AP001059 Genomic DNA. No translation available.
    AP001060 Genomic DNA. No translation available.
    CH471079 Genomic DNA. Translation: EAX09445.1 .
    BC002560 mRNA. Translation: AAH02560.1 .
    CCDSi CCDS13705.1. [Q9UJW3-2 ]
    CCDS46650.1. [Q9UJW3-1 ]
    RefSeqi NP_037501.2. NM_013369.3. [Q9UJW3-2 ]
    NP_787063.1. NM_175867.2. [Q9UJW3-1 ]
    UniGenei Hs.592165.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2PV0 X-ray 3.30 A/B/C 1-386 [» ]
    2PVC X-ray 3.69 A/B/C 1-386 [» ]
    2QRV X-ray 2.89 B/C/F/G 160-386 [» ]
    ProteinModelPortali Q9UJW3.
    SMRi Q9UJW3. Positions 34-380.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 118984. 11 interactions.
    DIPi DIP-35238N.
    IntActi Q9UJW3. 7 interactions.
    MINTi MINT-1448248.
    STRINGi 9606.ENSP00000270172.

    Protein family/group databases

    REBASEi 4636. M.HsaDnmt3L.

    PTM databases

    PhosphoSitei Q9UJW3.

    Polymorphism databases

    DMDMi 334302913.

    Proteomic databases

    PaxDbi Q9UJW3.
    PRIDEi Q9UJW3.

    Protocols and materials databases

    DNASUi 29947.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000270172 ; ENSP00000270172 ; ENSG00000142182 . [Q9UJW3-2 ]
    GeneIDi 29947.
    KEGGi hsa:29947.
    UCSCi uc002zeg.2. human. [Q9UJW3-1 ]
    uc002zeh.2. human. [Q9UJW3-2 ]

    Organism-specific databases

    CTDi 29947.
    GeneCardsi GC21M045666.
    HGNCi HGNC:2980. DNMT3L.
    MIMi 606588. gene.
    neXtProti NX_Q9UJW3.
    PharmGKBi PA27447.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG69419.
    HOGENOMi HOG000246422.
    HOVERGENi HBG051382.
    InParanoidi Q9UJW3.
    KOi K17400.
    OMAi TVPVWKR.
    TreeFami TF329039.

    Miscellaneous databases

    EvolutionaryTracei Q9UJW3.
    GeneWikii DNMT3L.
    GenomeRNAii 29947.
    NextBioi 52621.
    PROi Q9UJW3.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q9UJW3.
    Bgeei Q9UJW3.
    CleanExi HS_DNMT3L.
    Genevestigatori Q9UJW3.

    Family and domain databases

    Gene3Di 3.30.40.10. 1 hit.
    InterProi IPR025766. ADD.
    IPR011011. Znf_FYVE_PHD.
    IPR013083. Znf_RING/FYVE/PHD.
    [Graphical view ]
    SUPFAMi SSF57903. SSF57903. 1 hit.
    PROSITEi PS51533. ADD. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Isolation and initial characterization of a novel zinc finger gene, DNMT3L, on 21q22.3, related to the cytosine-5-methyltransferase 3 gene family."
      Aapola U., Shibuya K., Scott H.S., Ollila J., Vihinen M., Heino M., Shintani A., Kawasaki K., Minoshima S., Krohn K., Antonarakis S.E., Shimizu N., Kudoh J., Peterson P.
      Genomics 65:293-298(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), ALTERNATIVE SPLICING.
    2. "The DNA sequence of human chromosome 21."
      Hattori M., Fujiyama A., Taylor T.D., Watanabe H., Yada T., Park H.-S., Toyoda A., Ishii K., Totoki Y., Choi D.-K., Groner Y., Soeda E., Ohki M., Takagi T., Sakaki Y., Taudien S., Blechschmidt K., Polley A.
      , Menzel U., Delabar J., Kumpf K., Lehmann R., Patterson D., Reichwald K., Rump A., Schillhabel M., Schudy A., Zimmermann W., Rosenthal A., Kudoh J., Shibuya K., Kawasaki K., Asakawa S., Shintani A., Sasaki T., Nagamine K., Mitsuyama S., Antonarakis S.E., Minoshima S., Shimizu N., Nordsiek G., Hornischer K., Brandt P., Scharfe M., Schoen O., Desario A., Reichelt J., Kauer G., Bloecker H., Ramser J., Beck A., Klages S., Hennig S., Riesselmann L., Dagand E., Wehrmeyer S., Borzym K., Gardiner K., Nizetic D., Francis F., Lehrach H., Reinhardt R., Yaspo M.-L.
      Nature 405:311-319(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    4. "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 1), VARIANT GLY-278.
      Tissue: Placenta.
    5. "DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA."
      Ooi S.K., Qiu C., Bernstein E., Li K., Jia D., Yang Z., Erdjument-Bromage H., Tempst P., Lin S.-P., Allis C.D., Cheng X., Bestor T.H.
      Nature 448:714-717(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS), FUNCTION, HOMODIMERIZATION.
    6. "Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation."
      Jia D., Jurkowska R.Z., Zhang X., Jeltsch A., Cheng X.
      Nature 449:248-251(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.89 ANGSTROMS) OF 160-387, SUBUNIT, MUTAGENESIS OF PHE-261.

    Entry informationi

    Entry nameiDNM3L_HUMAN
    AccessioniPrimary (citable) accession number: Q9UJW3
    Secondary accession number(s): E9PB42, Q9BUJ4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 26, 2001
    Last sequence update: May 31, 2011
    Last modified: October 1, 2014
    This is version 119 of the entry and version 3 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

    Miscellaneous

    Interaction with histone H3 is strongly inhibited by methylation at lysine 4 (H3K4me).

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome 21
      Human chromosome 21: 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. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    6. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3