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Q8N488

- RYBP_HUMAN

UniProt

Q8N488 - RYBP_HUMAN

Protein

RING1 and YY1-binding protein

Gene

RYBP

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 108 (01 Oct 2014)
      Sequence version 2 (10 May 2005)
      Previous versions | rss
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    Functioni

    Inhibits ubiquitination and subsequent degradation of TP53, and thereby plays a role in regulating transcription of TP53 target genes. May be implicated in the regulation of the transcription as a repressor of the transcriptional activity of E4TF1. May bind to DNA. Promotes apoptosis.4 Publications

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri21 – 5030RanBP2-typePROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. DNA binding Source: UniProtKB-KW
    2. protein binding Source: UniProtKB
    3. transcription corepressor activity Source: ProtInc
    4. zinc ion binding Source: InterPro

    GO - Biological processi

    1. apoptotic process Source: UniProtKB-KW
    2. histone H2A monoubiquitination Source: UniProtKB
    3. multicellular organismal development Source: ProtInc
    4. negative regulation of transcription from RNA polymerase II promoter Source: ProtInc
    5. transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Molecular functioni

    Repressor

    Keywords - Biological processi

    Apoptosis, Transcription, Transcription regulation

    Keywords - Ligandi

    DNA-binding, Metal-binding, Zinc

    Enzyme and pathway databases

    SignaLinkiQ8N488.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    RING1 and YY1-binding protein
    Alternative name(s):
    Apoptin-associating protein 1
    Short name:
    APAP-1
    Death effector domain-associated factor
    Short name:
    DED-associated factor
    YY1 and E4TF1-associated factor 1
    Gene namesi
    Name:RYBP
    Synonyms:DEDAF, YEAF1
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 3

    Organism-specific databases

    HGNCiHGNC:10480. RYBP.

    Subcellular locationi

    Nucleus. Cytoplasm. Nucleusnucleoplasm By similarity
    Note: Primarily found in the nucleus. Detected in a punctate pattern likely to represent Polycomb group (PcG) bodies By similarity.By similarity

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell
    2. nucleoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA34893.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 228228RING1 and YY1-binding proteinPRO_0000097550Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei99 – 991Phosphoserine2 Publications
    Modified residuei127 – 1271Phosphoserine1 Publication
    Modified residuei130 – 1301Phosphoserine2 Publications
    Modified residuei227 – 2271Phosphoserine1 Publication

    Post-translational modificationi

    Monoubiquitinated.By similarity

    Keywords - PTMi

    Phosphoprotein, Ubl conjugation

    Proteomic databases

    MaxQBiQ8N488.
    PaxDbiQ8N488.
    PRIDEiQ8N488.

    PTM databases

    PhosphoSiteiQ8N488.

    Expressioni

    Tissue specificityi

    Widely expressed with highest levels in lymphoid tissues and placenta.3 Publications

    Gene expression databases

    BgeeiQ8N488.
    CleanExiHS_RYBP.
    GenevestigatoriQ8N488.

    Organism-specific databases

    HPAiHPA053357.

    Interactioni

    Subunit structurei

    Monomer. Interacts with apoptin, DEDD, FADD, CASP8, CASP10, YY1 and GABPB1. Component of repressive BCOR complex containing Polycomb group subcomplex at least composed of BCOR, PCGF1, RING1 and RNF2/RING2. Together with GABPB1 and YY1, it forms a ternary complex, probably being the bridge factor between these two transcription factors. Interacts with CBX2, YAF2, RING1 and RNF2. Interacts with ubiquitin and ubiquitinated proteins. Interacts with ubiquitinated histone H2A By similarity. Interacts with MDM2, and thereby inhibits ubiquitination of TP53. Identified in a ternary complex containing MDM2, TP53 and RYBP.By similarity6 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    MDM2Q0098711EBI-752324,EBI-389668
    RING1Q065872EBI-752324,EBI-752313
    TP53P046373EBI-752324,EBI-366083
    UBCP0CG483EBI-752324,EBI-3390054

    Protein-protein interaction databases

    BioGridi116997. 43 interactions.
    DIPiDIP-41435N.
    IntActiQ8N488. 10 interactions.
    MINTiMINT-158357.
    STRINGi9606.ENSP00000419494.

    Structurei

    Secondary structure

    1
    228
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi149 – 16315
    Beta strandi166 – 17510

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3IXSX-ray1.70B/D/F/H/J/L145-179[»]
    DisProtiDP00694.
    ProteinModelPortaliQ8N488.
    SMRiQ8N488. Positions 21-60, 145-176.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ8N488.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni143 – 22684Interaction with E4TF1BAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi73 – 764Poly-Pro
    Compositional biasi77 – 11943Lys-richAdd
    BLAST
    Compositional biasi179 – 21436Ser-richAdd
    BLAST

    Domaini

    Intrinsically unstructured in the absence of binding partners. Folds upon binding to DNA or RNF2 By similarity.By similarity

    Sequence similaritiesi

    Contains 1 RanBP2-type zinc finger.PROSITE-ProRule annotation

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri21 – 5030RanBP2-typePROSITE-ProRule annotationAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiNOG328071.
    HOVERGENiHBG001768.
    InParanoidiQ8N488.
    KOiK11469.
    OrthoDBiEOG7B8S61.
    PhylomeDBiQ8N488.
    TreeFamiTF350501.

    Family and domain databases

    InterProiIPR001876. Znf_RanBP2.
    [Graphical view]
    PfamiPF00641. zf-RanBP. 1 hit.
    [Graphical view]
    SMARTiSM00547. ZnF_RBZ. 1 hit.
    [Graphical view]
    PROSITEiPS01358. ZF_RANBP2_1. 1 hit.
    PS50199. ZF_RANBP2_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q8N488-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTMGDKKSPT RPKRQAKPAA DEGFWDCSVC TFRNSAEAFK CSICDVRKGT    50
    STRKPRINSQ LVAQQVAQQY ATPPPPKKEK KEKVEKQDKE KPEKDKEISP 100
    SVTKKNTNKK TKPKSDILKD PPSEANSIQS ANATTKTSET NHTSRPRLKN 150
    VDRSTAQQLA VTVGNVTVII TDFKEKTRSS STSSSTVTSS AGSEQQNQSS 200
    SGSESTDKGS SRSSTPKGDM SAVNDESF 228
    Length:228
    Mass (Da):24,822
    Last modified:May 10, 2005 - v2
    Checksum:iEB9593460A3F0F4C
    GO

    Sequence cautioni

    The sequence AAK63197.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.
    The sequence AAO73587.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.
    The sequence BAA89486.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti20 – 201A → T in AAH36459. (PubMed:15489334)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF179286 mRNA. Translation: AAD51858.1.
    AB029551 mRNA. Translation: BAA89486.1. Different initiation.
    AY228125 mRNA. Translation: AAO73587.1. Different initiation.
    AF227959 mRNA. Translation: AAK63197.1. Different initiation.
    BC014959 mRNA. Translation: AAH14959.1.
    BC036459 mRNA. Translation: AAH36459.1.
    RefSeqiNP_036366.3. NM_012234.6.
    UniGeneiHs.7910.

    Genome annotation databases

    EnsembliENST00000477973; ENSP00000419494; ENSG00000163602.
    GeneIDi23429.
    KEGGihsa:23429.
    UCSCiuc003dpe.3. human.

    Polymorphism databases

    DMDMi78102506.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF179286 mRNA. Translation: AAD51858.1 .
    AB029551 mRNA. Translation: BAA89486.1 . Different initiation.
    AY228125 mRNA. Translation: AAO73587.1 . Different initiation.
    AF227959 mRNA. Translation: AAK63197.1 . Different initiation.
    BC014959 mRNA. Translation: AAH14959.1 .
    BC036459 mRNA. Translation: AAH36459.1 .
    RefSeqi NP_036366.3. NM_012234.6.
    UniGenei Hs.7910.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3IXS X-ray 1.70 B/D/F/H/J/L 145-179 [» ]
    DisProti DP00694.
    ProteinModelPortali Q8N488.
    SMRi Q8N488. Positions 21-60, 145-176.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 116997. 43 interactions.
    DIPi DIP-41435N.
    IntActi Q8N488. 10 interactions.
    MINTi MINT-158357.
    STRINGi 9606.ENSP00000419494.

    PTM databases

    PhosphoSitei Q8N488.

    Polymorphism databases

    DMDMi 78102506.

    Proteomic databases

    MaxQBi Q8N488.
    PaxDbi Q8N488.
    PRIDEi Q8N488.

    Protocols and materials databases

    DNASUi 23429.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000477973 ; ENSP00000419494 ; ENSG00000163602 .
    GeneIDi 23429.
    KEGGi hsa:23429.
    UCSCi uc003dpe.3. human.

    Organism-specific databases

    CTDi 23429.
    GeneCardsi GC03M072506.
    HGNCi HGNC:10480. RYBP.
    HPAi HPA053357.
    MIMi 607535. gene.
    neXtProti NX_Q8N488.
    PharmGKBi PA34893.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG328071.
    HOVERGENi HBG001768.
    InParanoidi Q8N488.
    KOi K11469.
    OrthoDBi EOG7B8S61.
    PhylomeDBi Q8N488.
    TreeFami TF350501.

    Enzyme and pathway databases

    SignaLinki Q8N488.

    Miscellaneous databases

    ChiTaRSi RYBP. human.
    EvolutionaryTracei Q8N488.
    GeneWikii RYBP.
    GenomeRNAii 23429.
    NextBioi 45669.
    PROi Q8N488.
    SOURCEi Search...

    Gene expression databases

    Bgeei Q8N488.
    CleanExi HS_RYBP.
    Genevestigatori Q8N488.

    Family and domain databases

    InterProi IPR001876. Znf_RanBP2.
    [Graphical view ]
    Pfami PF00641. zf-RanBP. 1 hit.
    [Graphical view ]
    SMARTi SM00547. ZnF_RBZ. 1 hit.
    [Graphical view ]
    PROSITEi PS01358. ZF_RANBP2_1. 1 hit.
    PS50199. ZF_RANBP2_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The death effector domain-associated factor plays distinct regulatory roles in the nucleus and cytoplasm."
      Zheng L., Schickling O., Peter M.E., Lenardo M.J.
      J. Biol. Chem. 276:31945-31952(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION, INTERACTION WITH DEDD; FADD; CASP8 AND CASP10.
    2. "YEAF1/RYBP and YAF-2 are functionally distinct members of a cofactor family for the YY1 and E4TF1/hGABP transcription factors."
      Sawa C., Yoshikawa T., Matsuda-Suzuki F., Delehouzee S., Goto M., Watanabe H., Sawada J., Kataoka K., Handa H.
      J. Biol. Chem. 277:22484-22490(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION, INTERACTION WITH YY1 AND GABPB1.
    3. "Human death effector domain-associated factor interacts with the viral apoptosis agonist Apoptin and exerts tumor-preferential cell killing."
      Danen-van Oorschot A.A.M.M., Voskamp P., Seelen M.C.M.J., van Miltenburg M.H.A.M., Bolk M.W., Tait S.W., Boesen-de Cock J.G.R., Rohn J.L., Borst J., Noteborn M.H.M.
      Cell Death Differ. 11:564-573(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION, INTERACTION WITH APOPTIN.
    4. "The chicken anemia virus protein apoptin is associated with a human apoptotic protein, APAP1."
      Cheng C.M., Yuo C.Y.
      Submitted (JAN-2000) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    5. "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: Brain and Muscle.
    6. "Polycomb group and SCF ubiquitin ligases are found in a novel BCOR complex that is recruited to BCL6 targets."
      Gearhart M.D., Corcoran C.M., Wamstad J.A., Bardwell V.J.
      Mol. Cell. Biol. 26:6880-6889(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH BCOR; PCGF1; RING1 AND RNF2.
    7. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-130, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Cervix carcinoma.
    8. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
      Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
      Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    9. Cited for: FUNCTION, INTERACTION WITH MDM2, IDENTIFICATION IN A COMPLEX WITH MDM2 AND TP53.
    10. "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
      Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
      Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-127 AND SER-130, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Leukemic T-cell.
    11. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
      Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
      Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-99, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Cervix carcinoma.
    12. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    13. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
      Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
      Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-99 AND SER-227, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    14. "Polycomb group targeting through different binding partners of RING1B C-terminal domain."
      Wang R., Taylor A.B., Leal B.Z., Chadwell L.V., Ilangovan U., Robinson A.K., Schirf V., Hart P.J., Lafer E.M., Demeler B., Hinck A.P., McEwen D.G., Kim C.A.
      Structure 18:966-975(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 145-179 IN COMPLEX WITH RNF2/RING1B, INTERACTION WITH RNF2.

    Entry informationi

    Entry nameiRYBP_HUMAN
    AccessioniPrimary (citable) accession number: Q8N488
    Secondary accession number(s): Q9P2W5, Q9UMW4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 10, 2005
    Last sequence update: May 10, 2005
    Last modified: October 1, 2014
    This is version 108 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

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome 3
      Human chromosome 3: 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