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O96006

- ZBED1_HUMAN

UniProt

O96006 - ZBED1_HUMAN

Protein

Zinc finger BED domain-containing protein 1

Gene

ZBED1

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 115 (01 Oct 2014)
      Sequence version 1 (01 May 1999)
      Previous versions | rss
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    Functioni

    Binds to 5'-TGTCG[CT]GA[CT]A-3' DNA elements found in the promoter regions of a number of genes related to cell proliferation. Binds to the histone H1 promoter and stimulates transcription. Was first identified as gene weakly similar to Ac transposable elements, but does not code for any transposase activity.1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri20 – 7859BED-typePROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. DNA binding Source: UniProtKB-KW
    2. metal ion binding Source: UniProtKB-KW
    3. transposase activity Source: ProtInc

    GO - Biological processi

    1. metabolic process Source: GOC

    Keywords - Ligandi

    DNA-binding, Metal-binding, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Zinc finger BED domain-containing protein 1
    Alternative name(s):
    Putative Ac-like transposable element
    dREF homolog
    Gene namesi
    Name:ZBED1
    Synonyms:ALTE, DREF, KIAA0785, TRAMP
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome X

    Organism-specific databases

    HGNCiHGNC:447. ZBED1.

    Subcellular locationi

    Nucleus 1 Publication
    Note: In granular structures.

    GO - Cellular componenti

    1. nuclear chromosome Source: ProtInc

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA24753.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 694694Zinc finger BED domain-containing protein 1PRO_0000066560Add
    BLAST

    Proteomic databases

    MaxQBiO96006.
    PaxDbiO96006.
    PRIDEiO96006.

    PTM databases

    PhosphoSiteiO96006.

    Expressioni

    Tissue specificityi

    Ubiquitously expressed at low levels. Expression is highest in skeletal muscle, heart, spleen and placenta.

    Inductioni

    Expression is linked to the cell cycle: low in serum-starved fibroblasts, increasing during the G1/S phase, highest during the S/G2 phase and then decreasing again.1 Publication

    Gene expression databases

    ArrayExpressiO96006.
    BgeeiO96006.
    GenevestigatoriO96006.

    Organism-specific databases

    HPAiHPA038249.

    Interactioni

    Subunit structurei

    Homodimer.Curated

    Protein-protein interaction databases

    BioGridi114626. 22 interactions.
    IntActiO96006. 18 interactions.
    MINTiMINT-1436617.
    STRINGi9606.ENSP00000370616.

    Structurei

    Secondary structure

    1
    694
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi27 – 293
    Beta strandi35 – 373
    Helixi39 – 413
    Turni48 – 514
    Helixi61 – 699
    Helixi72 – 787

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2CT5NMR-A23-82[»]
    ProteinModelPortaliO96006.
    SMRiO96006. Positions 24-83, 164-647.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO96006.

    Family & Domainsi

    Sequence similaritiesi

    Contains 1 BED-type zinc finger.PROSITE-ProRule annotation

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri20 – 7859BED-typePROSITE-ProRule annotationAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiNOG317219.
    HOGENOMiHOG000155760.
    HOVERGENiHBG079365.
    InParanoidiO96006.
    OMAiLAEATWC.
    OrthoDBiEOG7KM5S5.
    PhylomeDBiO96006.
    TreeFamiTF322818.

    Family and domain databases

    InterProiIPR008906. HATC_dom_C.
    IPR012337. RNaseH-like_dom.
    IPR003656. Znf_BED_prd.
    [Graphical view]
    PfamiPF05699. Dimer_Tnp_hAT. 1 hit.
    PF02892. zf-BED. 1 hit.
    [Graphical view]
    SMARTiSM00614. ZnF_BED. 1 hit.
    [Graphical view]
    SUPFAMiSSF53098. SSF53098. 1 hit.
    PROSITEiPS50808. ZF_BED. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    O96006-1 [UniParc]FASTAAdd to Basket

    « Hide

    MENKSLESSQ TDLKLVAHPR AKSKVWKYFG FDTNAEGCIL QWKKIYCRIC    50
    MAQIAYSGNT SNLSYHLEKN HPEEFCEFVK SNTEQMREAF ATAFSKLKPE 100
    SSQQPGQDAL AVKAGHGYDS KKQQELTAAV LGLICEGLYP ASIVDEPTFK 150
    VLLKTADPRY ELPSRKYIST KAIPEKYGAV REVILKELAE ATWCGISTDM 200
    WRSENQNRAY VTLAAHFLGL GAPNCLSMGS RCLKTFEVPE ENTAETITRV 250
    LYEVFIEWGI SAKVFGATTN YGKDIVKACS LLDVAVHMPC LGHTFNAGIQ 300
    QAFQLPKLGA LLSRCRKLVE YFQQSAVAMY MLYEKQKQQN VAHCMLVSNR 350
    VSWWGSTLAM LQRLKEQQFV IAGVLVEDSN NHHLMLEASE WATIEGLVEL 400
    LQPFKQVAEM LSASRYPTIS MVKPLLHMLL NTTLNIKETD SKELSMAKEV 450
    IAKELSKTYQ ETPEIDMFLN VATFLDPRYK RLPFLSAFER QQVENRVVEE 500
    AKGLLDKVKD GGYRPAEDKI FPVPEEPPVK KLMRTSTPPP ASVINNMLAE 550
    IFCQTGGVED QEEWHAQVVE ELSNFKSQKV LGLNEDPLKW WSDRLALFPL 600
    LPKVLQKYWC VTATRVAPER LFGSAANVVS AKRNRLAPAH VDEQVFLYEN 650
    ARSGAEAEPE DQDEGEWGLD QEQVFSLGDG VSGGFFGIRD SSFL 694
    Length:694
    Mass (Da):78,156
    Last modified:May 1, 1999 - v1
    Checksum:i40404497B17283AF
    GO

    Sequence cautioni

    The sequence BAA34505.2 differs from that shown. Reason: Erroneous initiation.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti295 – 2951F → L in AAH15030. (PubMed:15489334)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Y16947 mRNA. Translation: CAA76545.1.
    Y17156 Genomic DNA. Translation: CAA76660.1.
    AB018328 mRNA. Translation: BAA34505.2. Different initiation.
    AC079176 Genomic DNA. No translation available.
    BC015030 mRNA. Translation: AAH15030.1.
    CCDSiCCDS14118.1.
    RefSeqiNP_001164606.1. NM_001171135.1.
    NP_001164607.1. NM_001171136.1.
    NP_004720.1. NM_004729.3.
    UniGeneiHs.131452.

    Genome annotation databases

    EnsembliENST00000381218; ENSP00000370616; ENSG00000214717.
    ENST00000381222; ENSP00000370620; ENSG00000214717.
    ENST00000381223; ENSP00000370621; ENSG00000214717.
    GeneIDi9189.
    KEGGihsa:9189.
    UCSCiuc004cqg.2. human.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Y16947 mRNA. Translation: CAA76545.1 .
    Y17156 Genomic DNA. Translation: CAA76660.1 .
    AB018328 mRNA. Translation: BAA34505.2 . Different initiation.
    AC079176 Genomic DNA. No translation available.
    BC015030 mRNA. Translation: AAH15030.1 .
    CCDSi CCDS14118.1.
    RefSeqi NP_001164606.1. NM_001171135.1.
    NP_001164607.1. NM_001171136.1.
    NP_004720.1. NM_004729.3.
    UniGenei Hs.131452.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2CT5 NMR - A 23-82 [» ]
    ProteinModelPortali O96006.
    SMRi O96006. Positions 24-83, 164-647.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 114626. 22 interactions.
    IntActi O96006. 18 interactions.
    MINTi MINT-1436617.
    STRINGi 9606.ENSP00000370616.

    PTM databases

    PhosphoSitei O96006.

    Proteomic databases

    MaxQBi O96006.
    PaxDbi O96006.
    PRIDEi O96006.

    Protocols and materials databases

    DNASUi 9189.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000381218 ; ENSP00000370616 ; ENSG00000214717 .
    ENST00000381222 ; ENSP00000370620 ; ENSG00000214717 .
    ENST00000381223 ; ENSP00000370621 ; ENSG00000214717 .
    GeneIDi 9189.
    KEGGi hsa:9189.
    UCSCi uc004cqg.2. human.

    Organism-specific databases

    CTDi 9189.
    GeneCardsi GC0XM002320.
    HGNCi HGNC:447. ZBED1.
    HPAi HPA038249.
    MIMi 300178. gene.
    neXtProti NX_O96006.
    PharmGKBi PA24753.
    HUGEi Search...
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG317219.
    HOGENOMi HOG000155760.
    HOVERGENi HBG079365.
    InParanoidi O96006.
    OMAi LAEATWC.
    OrthoDBi EOG7KM5S5.
    PhylomeDBi O96006.
    TreeFami TF322818.

    Miscellaneous databases

    EvolutionaryTracei O96006.
    GeneWikii ZBED1.
    GenomeRNAii 9189.
    NextBioi 34457.
    PROi O96006.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi O96006.
    Bgeei O96006.
    Genevestigatori O96006.

    Family and domain databases

    InterProi IPR008906. HATC_dom_C.
    IPR012337. RNaseH-like_dom.
    IPR003656. Znf_BED_prd.
    [Graphical view ]
    Pfami PF05699. Dimer_Tnp_hAT. 1 hit.
    PF02892. zf-BED. 1 hit.
    [Graphical view ]
    SMARTi SM00614. ZnF_BED. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53098. SSF53098. 1 hit.
    PROSITEi PS50808. ZF_BED. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "A novel pseudoautosomal human gene encodes a putative protein similar to Ac-like transposases."
      Esposito T., Gianfrancesco F., Ciccodicola A., Montanini L., Mumm S., D'Urso M., Forabosco A.
      Hum. Mol. Genet. 8:61-67(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].
      Tissue: Teratocarcinoma.
    2. "Prediction of the coding sequences of unidentified human genes. XI. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro."
      Nagase T., Ishikawa K., Suyama M., Kikuno R., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.
      DNA Res. 5:277-286(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Brain.
    3. "The DNA sequence of the human X chromosome."
      Ross M.T., Grafham D.V., Coffey A.J., Scherer S., McLay K., Muzny D., Platzer M., Howell G.R., Burrows C., Bird C.P., Frankish A., Lovell F.L., Howe K.L., Ashurst J.L., Fulton R.S., Sudbrak R., Wen G., Jones M.C.
      , Hurles M.E., Andrews T.D., Scott C.E., Searle S., Ramser J., Whittaker A., Deadman R., Carter N.P., Hunt S.E., Chen R., Cree A., Gunaratne P., Havlak P., Hodgson A., Metzker M.L., Richards S., Scott G., Steffen D., Sodergren E., Wheeler D.A., Worley K.C., Ainscough R., Ambrose K.D., Ansari-Lari M.A., Aradhya S., Ashwell R.I., Babbage A.K., Bagguley C.L., Ballabio A., Banerjee R., Barker G.E., Barlow K.F., Barrett I.P., Bates K.N., Beare D.M., Beasley H., Beasley O., Beck A., Bethel G., Blechschmidt K., Brady N., Bray-Allen S., Bridgeman A.M., Brown A.J., Brown M.J., Bonnin D., Bruford E.A., Buhay C., Burch P., Burford D., Burgess J., Burrill W., Burton J., Bye J.M., Carder C., Carrel L., Chako J., Chapman J.C., Chavez D., Chen E., Chen G., Chen Y., Chen Z., Chinault C., Ciccodicola A., Clark S.Y., Clarke G., Clee C.M., Clegg S., Clerc-Blankenburg K., Clifford K., Cobley V., Cole C.G., Conquer J.S., Corby N., Connor R.E., David R., Davies J., Davis C., Davis J., Delgado O., Deshazo D., Dhami P., Ding Y., Dinh H., Dodsworth S., Draper H., Dugan-Rocha S., Dunham A., Dunn M., Durbin K.J., Dutta I., Eades T., Ellwood M., Emery-Cohen A., Errington H., Evans K.L., Faulkner L., Francis F., Frankland J., Fraser A.E., Galgoczy P., Gilbert J., Gill R., Gloeckner G., Gregory S.G., Gribble S., Griffiths C., Grocock R., Gu Y., Gwilliam R., Hamilton C., Hart E.A., Hawes A., Heath P.D., Heitmann K., Hennig S., Hernandez J., Hinzmann B., Ho S., Hoffs M., Howden P.J., Huckle E.J., Hume J., Hunt P.J., Hunt A.R., Isherwood J., Jacob L., Johnson D., Jones S., de Jong P.J., Joseph S.S., Keenan S., Kelly S., Kershaw J.K., Khan Z., Kioschis P., Klages S., Knights A.J., Kosiura A., Kovar-Smith C., Laird G.K., Langford C., Lawlor S., Leversha M., Lewis L., Liu W., Lloyd C., Lloyd D.M., Loulseged H., Loveland J.E., Lovell J.D., Lozado R., Lu J., Lyne R., Ma J., Maheshwari M., Matthews L.H., McDowall J., McLaren S., McMurray A., Meidl P., Meitinger T., Milne S., Miner G., Mistry S.L., Morgan M., Morris S., Mueller I., Mullikin J.C., Nguyen N., Nordsiek G., Nyakatura G., O'dell C.N., Okwuonu G., Palmer S., Pandian R., Parker D., Parrish J., Pasternak S., Patel D., Pearce A.V., Pearson D.M., Pelan S.E., Perez L., Porter K.M., Ramsey Y., Reichwald K., Rhodes S., Ridler K.A., Schlessinger D., Schueler M.G., Sehra H.K., Shaw-Smith C., Shen H., Sheridan E.M., Shownkeen R., Skuce C.D., Smith M.L., Sotheran E.C., Steingruber H.E., Steward C.A., Storey R., Swann R.M., Swarbreck D., Tabor P.E., Taudien S., Taylor T., Teague B., Thomas K., Thorpe A., Timms K., Tracey A., Trevanion S., Tromans A.C., d'Urso M., Verduzco D., Villasana D., Waldron L., Wall M., Wang Q., Warren J., Warry G.L., Wei X., West A., Whitehead S.L., Whiteley M.N., Wilkinson J.E., Willey D.L., Williams G., Williams L., Williamson A., Williamson H., Wilming L., Woodmansey R.L., Wray P.W., Yen J., Zhang J., Zhou J., Zoghbi H., Zorilla S., Buck D., Reinhardt R., Poustka A., Rosenthal A., Lehrach H., Meindl A., Minx P.J., Hillier L.W., Willard H.F., Wilson R.K., Waterston R.H., Rice C.M., Vaudin M., Coulson A., Nelson D.L., Weinstock G., Sulston J.E., Durbin R.M., Hubbard T., Gibbs R.A., Beck S., Rogers J., Bentley D.R.
      Nature 434:325-337(2005) [PubMed] [Europe PMC] [Abstract]
      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].
      Tissue: Uterus.
    5. "Identification of a human homologue of the DREF transcription factor with a potential role in regulation of the histone H1 gene."
      Ohshima N., Takahashi M., Hirose F.
      J. Biol. Chem. 278:22928-22938(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INDUCTION, SUBCELLULAR LOCATION.
    6. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    7. "Solution structure of the zinc finger BED domain of the zinc finger BED domain containing protein 1."
      RIKEN structural genomics initiative (RSGI)
      Submitted (NOV-2005) to the PDB data bank
      Cited for: STRUCTURE BY NMR OF 23-82.

    Entry informationi

    Entry nameiZBED1_HUMAN
    AccessioniPrimary (citable) accession number: O96006
    Secondary accession number(s): Q96BY4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 16, 2004
    Last sequence update: May 1, 1999
    Last modified: October 1, 2014
    This is version 115 of the entry and version 1 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

    The gene coding for this protein is located in the pseudoautosomal region 1 (PAR1) of X and Y chromosomes.

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome X
      Human chromosome X: 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