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Q9NQX0

- PRDM6_HUMAN

UniProt

Q9NQX0 - PRDM6_HUMAN

Protein

Putative histone-lysine N-methyltransferase PRDM6

Gene

PRDM6

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 116 (01 Oct 2014)
      Sequence version 2 (10 Feb 2009)
      Previous versions | rss
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    Functioni

    Putative histone methyltransferase that acts as a transcriptional repressor of smooth muscle gene expression. Promotes the transition from differentiated to proliferative smooth muscle by suppressing differentiation and maintaining the proliferative potential of vascular smooth muscle cells. Also plays a role in endothelial cells by inhibiting endothelial cell proliferation, survival and differentiation. It is unclear whether it has histone methyltransferase activity in vivo. According to some authors, it does not act as a histone methyltransferase by itself and represses transcription by recruiting EHMT2/G9a. According to others, it possesses histone methyltransferase activity when associated with other proteins and specifically methylates 'Lys-20' of histone H4 in vitro. 'Lys-20' methylation represents a specific tag for epigenetic transcriptional repression By similarity.By similarity

    Catalytic activityi

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

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri473 – 49523C2H2-type 1; degeneratePROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri501 – 52323C2H2-type 2PROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri529 – 55123C2H2-type 3PROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri557 – 57923C2H2-type 4; degeneratePROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. histone-lysine N-methyltransferase activity Source: UniProtKB-EC
    2. metal ion binding Source: UniProtKB-KW
    3. nucleic acid binding Source: InterPro

    GO - Biological processi

    1. negative regulation of smooth muscle cell differentiation Source: Ensembl
    2. negative regulation of transcription, DNA-templated Source: Ensembl
    3. neurogenesis Source: Ensembl
    4. transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Molecular functioni

    Chromatin regulator, Methyltransferase, Repressor, Transferase

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

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

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Putative histone-lysine N-methyltransferase PRDM6 (EC:2.1.1.43)
    Alternative name(s):
    PR domain zinc finger protein 6
    PR domain-containing protein 6
    Gene namesi
    Name:PRDM6
    Synonyms:PFM3
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 5

    Organism-specific databases

    HGNCiHGNC:9350. PRDM6.

    Subcellular locationi

    Nucleus By similarity

    GO - Cellular componenti

    1. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA33718.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 595595Putative histone-lysine N-methyltransferase PRDM6PRO_0000047762Add
    BLAST

    Proteomic databases

    PaxDbiQ9NQX0.
    PRIDEiQ9NQX0.

    PTM databases

    PhosphoSiteiQ9NQX0.

    Expressioni

    Gene expression databases

    BgeeiQ9NQX0.
    CleanExiHS_PRDM6.
    GenevestigatoriQ9NQX0.

    Organism-specific databases

    HPAiHPA030322.
    HPA030324.

    Interactioni

    Subunit structurei

    Interacts with HDAC1, HDAC2, HDAC3, CBX1 and EP300.By similarity

    Structurei

    3D structure databases

    ProteinModelPortaliQ9NQX0.
    SMRiQ9NQX0. Positions 199-374, 473-577.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini246 – 365120SETPROSITE-ProRule annotationAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi47 – 7327Pro-richAdd
    BLAST
    Compositional biasi97 – 10610Poly-Ala
    Compositional biasi123 – 1297Poly-Ala
    Compositional biasi151 – 16212Poly-GlyAdd
    BLAST
    Compositional biasi228 – 2325Poly-Ala

    Sequence similaritiesi

    Belongs to the class V-like SAM-binding methyltransferase superfamily.PROSITE-ProRule annotation
    Contains 4 C2H2-type zinc fingers.PROSITE-ProRule annotation
    Contains 1 SET domain.PROSITE-ProRule annotation

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri473 – 49523C2H2-type 1; degeneratePROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri501 – 52323C2H2-type 2PROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri529 – 55123C2H2-type 3PROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri557 – 57923C2H2-type 4; degeneratePROSITE-ProRule annotationAdd
    BLAST

    Keywords - Domaini

    Repeat, Zinc-finger

    Phylogenomic databases

    eggNOGiNOG325470.
    HOGENOMiHOG000090218.
    HOVERGENiHBG108289.
    InParanoidiQ9NQX0.
    OMAiIVFPQTP.
    OrthoDBiEOG776SPN.
    PhylomeDBiQ9NQX0.
    TreeFamiTF106403.

    Family and domain databases

    Gene3Di3.30.160.60. 3 hits.
    InterProiIPR001214. SET_dom.
    IPR007087. Znf_C2H2.
    IPR015880. Znf_C2H2-like.
    IPR013087. Znf_C2H2/integrase_DNA-bd.
    [Graphical view]
    PfamiPF00856. SET. 1 hit.
    PF00096. zf-C2H2. 1 hit.
    [Graphical view]
    SMARTiSM00317. SET. 1 hit.
    SM00355. ZnF_C2H2. 4 hits.
    [Graphical view]
    PROSITEiPS50280. SET. 1 hit.
    PS00028. ZINC_FINGER_C2H2_1. 2 hits.
    PS50157. ZINC_FINGER_C2H2_2. 4 hits.
    [Graphical view]

    Sequences (3)i

    Sequence statusi: Complete.

    This entry describes 3 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q9NQX0-3) [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

    MLKPGDPGGS AFLKVDPAYL QHWQQLFPHG GAGPLKGSGA AGLLSAPQPL    50
    QPPPPPPPPE RAEPPPDSLR PRPASLSSAS STPASSSTSA SSASSCAAAA 100
    AAAALAGLSA LPVSQLPVFA PLAAAAVAAE PLPPKELCLG ATSGPGPVKC 150
    GGGGGGGGEG RGAPRFRCSA EELDYYLYGQ QRMEIIPLNQ HTSDPNNRCD 200
    MCADNRNGEC PMHGPLHSLR RLVGTSSAAA AAPPPELPEW LRDLPREVCL 250
    CTSTVPGLAY GICAAQRIQQ GTWIGPFQGV LLPPEKVQAG AVRNTQHLWE 300
    IYDQDGTLQH FIDGGEPSKS SWMRYIRCAR HCGEQNLTVV QYRSNIFYRA 350
    CIDIPRGTEL LVWYNDSYTS FFGIPLQCIA QDENLNVPST VMEAMCRQDA 400
    LQPFNKSSKL APTTQQRSVV FPQTPCSRNF SLLDKSGPIE SGFNQINVKN 450
    QRVLASPTST SQLHSEFSDW HLWKCGQCFK TFTQRILLQM HVCTQNPDRP 500
    YQCGHCSQSF SQPSELRNHV VTHSSDRPFK CGYCGRAFAG ATTLNNHIRT 550
    HTGEKPFKCE RCERSFTQAT QLSRHQRMPN ECKPITESPE SIEVD 595
    Length:595
    Mass (Da):64,452
    Last modified:February 10, 2009 - v2
    Checksum:iDB8D815E7C107451
    GO
    Isoform 2 (identifier: Q9NQX0-2) [UniParc]FASTAAdd to Basket

    Also known as: B

    The sequence of this isoform differs from the canonical sequence as follows:
         1-182: Missing.
         314-595: Missing.

    Show »
    Length:131
    Mass (Da):14,436
    Checksum:i1C608683110D5DC2
    GO
    Isoform 3 (identifier: Q9NQX0-1) [UniParc]FASTAAdd to Basket

    Also known as: A

    The sequence of this isoform differs from the canonical sequence as follows:
         1-182: Missing.

    Show »
    Length:413
    Mass (Da):46,635
    Checksum:i9D5FCB5B9F885666
    GO

    Sequence cautioni

    The sequence AAF78078.1 differs from that shown. Reason: Erroneous initiation.
    The sequence AAF78079.1 differs from that shown. Reason: Erroneous initiation.

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 182182Missing in isoform 2 and isoform 3. 1 PublicationVSP_036348Add
    BLAST
    Alternative sequencei314 – 595282Missing in isoform 2. 1 PublicationVSP_006929Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF272898 mRNA. Translation: AAF78078.1. Different initiation.
    AF272899 mRNA. Translation: AAF78079.1. Different initiation.
    AC008548 Genomic DNA. No translation available.
    AC106786 Genomic DNA. No translation available.
    CCDSiCCDS47259.1. [Q9NQX0-3]
    RefSeqiNP_001129711.1. NM_001136239.1. [Q9NQX0-3]
    XP_005272185.1. XM_005272128.2. [Q9NQX0-3]
    UniGeneiHs.135118.

    Genome annotation databases

    EnsembliENST00000407847; ENSP00000384725; ENSG00000061455. [Q9NQX0-3]
    GeneIDi93166.
    KEGGihsa:93166.
    UCSCiuc003kti.3. human. [Q9NQX0-3]

    Polymorphism databases

    DMDMi223590133.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF272898 mRNA. Translation: AAF78078.1 . Different initiation.
    AF272899 mRNA. Translation: AAF78079.1 . Different initiation.
    AC008548 Genomic DNA. No translation available.
    AC106786 Genomic DNA. No translation available.
    CCDSi CCDS47259.1. [Q9NQX0-3 ]
    RefSeqi NP_001129711.1. NM_001136239.1. [Q9NQX0-3 ]
    XP_005272185.1. XM_005272128.2. [Q9NQX0-3 ]
    UniGenei Hs.135118.

    3D structure databases

    ProteinModelPortali Q9NQX0.
    SMRi Q9NQX0. Positions 199-374, 473-577.
    ModBasei Search...
    MobiDBi Search...

    PTM databases

    PhosphoSitei Q9NQX0.

    Polymorphism databases

    DMDMi 223590133.

    Proteomic databases

    PaxDbi Q9NQX0.
    PRIDEi Q9NQX0.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000407847 ; ENSP00000384725 ; ENSG00000061455 . [Q9NQX0-3 ]
    GeneIDi 93166.
    KEGGi hsa:93166.
    UCSCi uc003kti.3. human. [Q9NQX0-3 ]

    Organism-specific databases

    CTDi 93166.
    GeneCardsi GC05P122424.
    HGNCi HGNC:9350. PRDM6.
    HPAi HPA030322.
    HPA030324.
    neXtProti NX_Q9NQX0.
    PharmGKBi PA33718.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG325470.
    HOGENOMi HOG000090218.
    HOVERGENi HBG108289.
    InParanoidi Q9NQX0.
    OMAi IVFPQTP.
    OrthoDBi EOG776SPN.
    PhylomeDBi Q9NQX0.
    TreeFami TF106403.

    Miscellaneous databases

    GenomeRNAii 93166.
    NextBioi 78013.
    PROi Q9NQX0.

    Gene expression databases

    Bgeei Q9NQX0.
    CleanExi HS_PRDM6.
    Genevestigatori Q9NQX0.

    Family and domain databases

    Gene3Di 3.30.160.60. 3 hits.
    InterProi IPR001214. SET_dom.
    IPR007087. Znf_C2H2.
    IPR015880. Znf_C2H2-like.
    IPR013087. Znf_C2H2/integrase_DNA-bd.
    [Graphical view ]
    Pfami PF00856. SET. 1 hit.
    PF00096. zf-C2H2. 1 hit.
    [Graphical view ]
    SMARTi SM00317. SET. 1 hit.
    SM00355. ZnF_C2H2. 4 hits.
    [Graphical view ]
    PROSITEi PS50280. SET. 1 hit.
    PS00028. ZINC_FINGER_C2H2_1. 2 hits.
    PS50157. ZINC_FINGER_C2H2_2. 4 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The yin-yang of PR-domain family genes in tumorigenesis."
      Jiang G.L., Huang S.
      Histol. Histopathol. 15:109-117(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 2 AND 3).
    2. "The DNA sequence and comparative analysis of human chromosome 5."
      Schmutz J., Martin J., Terry A., Couronne O., Grimwood J., Lowry S., Gordon L.A., Scott D., Xie G., Huang W., Hellsten U., Tran-Gyamfi M., She X., Prabhakar S., Aerts A., Altherr M., Bajorek E., Black S.
      , Branscomb E., Caoile C., Challacombe J.F., Chan Y.M., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Lopez F., Lou Y., Martinez D., Medina C., Morgan J., Nandkeshwar R., Noonan J.P., Pitluck S., Pollard M., Predki P., Priest J., Ramirez L., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wheeler J., Wu K., Yang J., Dickson M., Cheng J.-F., Eichler E.E., Olsen A., Pennacchio L.A., Rokhsar D.S., Richardson P., Lucas S.M., Myers R.M., Rubin E.M.
      Nature 431:268-274(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

    Entry informationi

    Entry nameiPRDM6_HUMAN
    AccessioniPrimary (citable) accession number: Q9NQX0
    Secondary accession number(s): B5MCJ4, Q9NQW9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 8, 2002
    Last sequence update: February 10, 2009
    Last modified: October 1, 2014
    This is version 116 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 5
      Human chromosome 5: entries, gene names and cross-references to MIM
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3