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Q8N488

- RYBP_HUMAN

UniProt

Q8N488 - RYBP_HUMAN

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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

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. transcription corepressor activity Source: ProtInc
  3. 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
Complete GO annotation...

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-KW
  2. nucleoplasm Source: Ensembl
Complete GO annotation...

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. 47 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

        10         20         30         40         50
MTMGDKKSPT RPKRQAKPAA DEGFWDCSVC TFRNSAEAFK CSICDVRKGT
60 70 80 90 100
STRKPRINSQ LVAQQVAQQY ATPPPPKKEK KEKVEKQDKE KPEKDKEISP
110 120 130 140 150
SVTKKNTNKK TKPKSDILKD PPSEANSIQS ANATTKTSET NHTSRPRLKN
160 170 180 190 200
VDRSTAQQLA VTVGNVTVII TDFKEKTRSS STSSSTVTSS AGSEQQNQSS
210 220
SGSESTDKGS SRSSTPKGDM SAVNDESF
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. 47 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 GC03M072420.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 109 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