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Q9UKN5

- PRDM4_HUMAN

UniProt

Q9UKN5 - PRDM4_HUMAN

Protein

PR domain zinc finger protein 4

Gene

PRDM4

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 130 (01 Oct 2014)
      Sequence version 3 (08 Nov 2002)
      Previous versions | rss
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    Functioni

    May function as a transcription factor involved in cell differentiation.

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri545 – 56622C2H2-type 1; atypicalPROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri618 – 64023C2H2-type 2PROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri646 – 66823C2H2-type 3PROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri674 – 69623C2H2-type 4PROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri702 – 72423C2H2-type 5PROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri730 – 75223C2H2-type 6; atypicalPROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. DNA binding Source: UniProtKB-KW
    2. methyltransferase activity Source: UniProtKB-KW
    3. zinc ion binding Source: ProtInc

    GO - Biological processi

    1. cell proliferation Source: ProtInc
    2. negative regulation of cell cycle Source: Reactome
    3. neurotrophin TRK receptor signaling pathway Source: Reactome
    4. regulation of transcription, DNA-templated Source: UniProtKB-KW
    5. signal transduction Source: ProtInc
    6. transcription from RNA polymerase II promoter Source: ProtInc

    Keywords - Molecular functioni

    Methyltransferase, Transferase

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

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

    Enzyme and pathway databases

    ReactomeiREACT_13695. p75NTR negatively regulates cell cycle via SC1.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    PR domain zinc finger protein 4 (EC:2.1.1.-)
    Alternative name(s):
    PR domain-containing protein 4
    Gene namesi
    Name:PRDM4
    Synonyms:PFM1
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 12

    Organism-specific databases

    HGNCiHGNC:9348. PRDM4.

    Subcellular locationi

    Nucleus Curated

    GO - Cellular componenti

    1. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA33716.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 801801PR domain zinc finger protein 4PRO_0000047760Add
    BLAST

    Proteomic databases

    PaxDbiQ9UKN5.
    PRIDEiQ9UKN5.

    PTM databases

    PhosphoSiteiQ9UKN5.

    Expressioni

    Tissue specificityi

    Expressed in many tissues. Highly expressed in ovary, testis, pancreas, brain, heart and prostate.

    Gene expression databases

    ArrayExpressiQ9UKN5.
    BgeeiQ9UKN5.
    CleanExiHS_PRDM4.
    GenevestigatoriQ9UKN5.

    Organism-specific databases

    HPAiHPA024322.

    Interactioni

    Protein-protein interaction databases

    BioGridi116288. 10 interactions.
    IntActiQ9UKN5. 3 interactions.
    MINTiMINT-1183894.
    STRINGi9606.ENSP00000228437.

    Structurei

    Secondary structure

    1
    801
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi374 – 3774
    Helixi378 – 3803
    Beta strandi382 – 3887
    Turni389 – 3913
    Helixi405 – 4084
    Beta strandi414 – 4185
    Beta strandi425 – 4317
    Beta strandi445 – 4473
    Beta strandi462 – 4687
    Beta strandi471 – 4777
    Turni481 – 4833
    Helixi486 – 4894
    Turni496 – 4983
    Beta strandi501 – 5066
    Beta strandi509 – 5168
    Beta strandi525 – 5284

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2L9ZNMR-A366-402[»]
    3DB5X-ray2.15A/B390-540[»]
    ProteinModelPortaliQ9UKN5.
    SMRiQ9UKN5. Positions 365-801.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9UKN5.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini412 – 529118SETPROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the class V-like SAM-binding methyltransferase superfamily.PROSITE-ProRule annotation
    Contains 6 C2H2-type zinc fingers.PROSITE-ProRule annotation
    Contains 1 SET domain.PROSITE-ProRule annotation

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri545 – 56622C2H2-type 1; atypicalPROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri618 – 64023C2H2-type 2PROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri646 – 66823C2H2-type 3PROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri674 – 69623C2H2-type 4PROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri702 – 72423C2H2-type 5PROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri730 – 75223C2H2-type 6; atypicalPROSITE-ProRule annotationAdd
    BLAST

    Keywords - Domaini

    Repeat, Zinc-finger

    Phylogenomic databases

    eggNOGiCOG5048.
    HOGENOMiHOG000060213.
    HOVERGENiHBG053672.
    InParanoidiQ9UKN5.
    KOiK12463.
    OMAiVLEFCII.
    OrthoDBiEOG7R830T.
    PhylomeDBiQ9UKN5.
    TreeFamiTF332513.

    Family and domain databases

    Gene3Di3.30.160.60. 6 hits.
    InterProiIPR001214. SET_dom.
    IPR007087. Znf_C2H2.
    IPR015880. Znf_C2H2-like.
    IPR013087. Znf_C2H2/integrase_DNA-bd.
    IPR017124. Znf_PRDM4.
    [Graphical view]
    PfamiPF00096. zf-C2H2. 1 hit.
    [Graphical view]
    PIRSFiPIRSF037161. PRDM4. 1 hit.
    SMARTiSM00317. SET. 1 hit.
    SM00355. ZnF_C2H2. 7 hits.
    [Graphical view]
    PROSITEiPS50280. SET. 1 hit.
    PS00028. ZINC_FINGER_C2H2_1. 5 hits.
    PS50157. ZINC_FINGER_C2H2_2. 6 hits.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q9UKN5-1 [UniParc]FASTAAdd to Basket

    « Hide

    MHHRMNEMNL SPVGMEQLTS SSVSNALPVS GSHLGLAASP THSAIPAPGL    50
    PVAIPNLGPS LSSLPSALSL MLPMGIGDRG VMCGLPERNY TLPPPPYPHL 100
    ESSYFRTILP GILSYLADRP PPQYIHPNSI NVDGNTALSI TNNPSALDPY 150
    QSNGNVGLEP GIVSIDSRSV NTHGAQSLHP SDGHEVALDT AITMENVSRV 200
    TSPISTDGMA EELTMDGVAG EHSQIPNGSR SHEPLSVDSV SNNLAADAVG 250
    HGGVIPMHGN GLELPVVMET DHIASRVNGM SDSALSDSIH TVAMSTNSVS 300
    VALSTSHNLA SLESVSLHEV GLSLEPVAVS SITQEVAMGT GHVDVSSDSL 350
    SFVSPSLQME DSNSNKENMA TLFTIWCTLC DRAYPSDCPE HGPVTFVPDT 400
    PIESRARLSL PKQLVLRQSI VGAEVGVWTG ETIPVRTCFG PLIGQQSHSM 450
    EVAEWTDKAV NHIWKIYHNG VLEFCIITTD ENECNWMMFV RKARNREEQN 500
    LVAYPHDGKI FFCTSQDIPP ENELLFYYSR DYAQQIGVPE HPDVHLCNCG 550
    KECNSYTEFK AHLTSHIHNH LPTQGHSGSH GPSHSKERKW KCSMCPQAFI 600
    SPSKLHVHFM GHMGMKPHKC DFCSKAFSDP SNLRTHLKIH TGQKNYRCTL 650
    CDKSFTQKAH LESHMVIHTG EKNLKCDYCD KLFMRRQDLK QHVLIHTQER 700
    QIKCPKCDKL FLRTNHLKKH LNSHEGKRDY VCEKCTKAYL TKYHLTRHLK 750
    TCKGPTSSSS APEEEEEDDS EEEDLADSVG TEDCRINSAV YSADESLSAH 800
    K 801
    Length:801
    Mass (Da):87,920
    Last modified:November 8, 2002 - v3
    Checksum:i13B9B94F0825D113
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti16 – 161E → A in AAD55249. (PubMed:10552934)Curated
    Sequence conflicti580 – 5801H → I in AAD55249. (PubMed:10552934)Curated
    Sequence conflicti608 – 6081H → Y in AAD55249. (PubMed:10552934)Curated
    Sequence conflicti662 – 6632ES → GV in AAD55249. (PubMed:10552934)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF144757 mRNA. Translation: AAD55249.2.
    BC035581 mRNA. Translation: AAH35581.1.
    AL133083 mRNA. Translation: CAB61401.1.
    CCDSiCCDS9115.1.
    PIRiT42688.
    RefSeqiNP_036538.3. NM_012406.3.
    UniGeneiHs.506655.

    Genome annotation databases

    EnsembliENST00000228437; ENSP00000228437; ENSG00000110851.
    GeneIDi11108.
    KEGGihsa:11108.
    UCSCiuc001tmp.3. human.

    Polymorphism databases

    DMDMi25008960.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF144757 mRNA. Translation: AAD55249.2 .
    BC035581 mRNA. Translation: AAH35581.1 .
    AL133083 mRNA. Translation: CAB61401.1 .
    CCDSi CCDS9115.1.
    PIRi T42688.
    RefSeqi NP_036538.3. NM_012406.3.
    UniGenei Hs.506655.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2L9Z NMR - A 366-402 [» ]
    3DB5 X-ray 2.15 A/B 390-540 [» ]
    ProteinModelPortali Q9UKN5.
    SMRi Q9UKN5. Positions 365-801.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 116288. 10 interactions.
    IntActi Q9UKN5. 3 interactions.
    MINTi MINT-1183894.
    STRINGi 9606.ENSP00000228437.

    PTM databases

    PhosphoSitei Q9UKN5.

    Polymorphism databases

    DMDMi 25008960.

    Proteomic databases

    PaxDbi Q9UKN5.
    PRIDEi Q9UKN5.

    Protocols and materials databases

    DNASUi 11108.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000228437 ; ENSP00000228437 ; ENSG00000110851 .
    GeneIDi 11108.
    KEGGi hsa:11108.
    UCSCi uc001tmp.3. human.

    Organism-specific databases

    CTDi 11108.
    GeneCardsi GC12M108126.
    HGNCi HGNC:9348. PRDM4.
    HPAi HPA024322.
    MIMi 605780. gene.
    neXtProti NX_Q9UKN5.
    PharmGKBi PA33716.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG5048.
    HOGENOMi HOG000060213.
    HOVERGENi HBG053672.
    InParanoidi Q9UKN5.
    KOi K12463.
    OMAi VLEFCII.
    OrthoDBi EOG7R830T.
    PhylomeDBi Q9UKN5.
    TreeFami TF332513.

    Enzyme and pathway databases

    Reactomei REACT_13695. p75NTR negatively regulates cell cycle via SC1.

    Miscellaneous databases

    EvolutionaryTracei Q9UKN5.
    GenomeRNAii 11108.
    NextBioi 42234.
    PROi Q9UKN5.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q9UKN5.
    Bgeei Q9UKN5.
    CleanExi HS_PRDM4.
    Genevestigatori Q9UKN5.

    Family and domain databases

    Gene3Di 3.30.160.60. 6 hits.
    InterProi IPR001214. SET_dom.
    IPR007087. Znf_C2H2.
    IPR015880. Znf_C2H2-like.
    IPR013087. Znf_C2H2/integrase_DNA-bd.
    IPR017124. Znf_PRDM4.
    [Graphical view ]
    Pfami PF00096. zf-C2H2. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF037161. PRDM4. 1 hit.
    SMARTi SM00317. SET. 1 hit.
    SM00355. ZnF_C2H2. 7 hits.
    [Graphical view ]
    PROSITEi PS50280. SET. 1 hit.
    PS00028. ZINC_FINGER_C2H2_1. 5 hits.
    PS50157. ZINC_FINGER_C2H2_2. 6 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "PFM1 (PRDM4), a new member of the PR-domain family, maps to a tumor suppressor locus on human chromosome 12q23-q24.1."
      Yang X.-H., Huang S.
      Genomics 61:319-325(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    2. "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].
      Tissue: Testis.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 77-801.
      Tissue: Testis.
    4. "The crystal structure of methyltransferase domain of human PR domain-containing protein 4."
      Structural genomics consortium (SGC)
      Submitted (AUG-2008) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) OF 390-540.

    Entry informationi

    Entry nameiPRDM4_HUMAN
    AccessioniPrimary (citable) accession number: Q9UKN5
    Secondary accession number(s): Q9UFA6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 16, 2001
    Last sequence update: November 8, 2002
    Last modified: October 1, 2014
    This is version 130 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

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome 12
      Human chromosome 12: entries, gene names and cross-references to MIM
    2. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3