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Protein

RING1 and YY1-binding protein

Gene

Rybp

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: 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 (By similarity).By similarity2 Publications

Regions

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

GO - Molecular functioni

  • DNA binding Source: MGI
  • transcription corepressor activity Source: MGI
  • zinc ion binding Source: InterPro

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

Apoptosis, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
RING1 and YY1-binding protein
Alternative name(s):
Death effector domain-associated factor
Short name:
DED-associated factor
Gene namesi
Name:Rybp
Synonyms:Dedaf
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 6

Organism-specific databases

MGIiMGI:1929059. Rybp.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • nucleoplasm Source: MGI
  • nucleus Source: MGI
  • PcG protein complex Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Disruption phenotypei

Embryonically lethal. Embryos die at early postimplantation stage.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi31 – 322TF → AA: Loss of ubiquitin binding. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 228228RING1 and YY1-binding proteinPRO_0000097551Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei99 – 991PhosphoserineBy similarity
Modified residuei123 – 1231PhosphoserineCombined sources
Modified residuei127 – 1271PhosphoserineCombined sources
Modified residuei130 – 1301PhosphoserineCombined sources
Modified residuei227 – 2271PhosphoserineBy similarity

Post-translational modificationi

Monoubiquitinated.

Keywords - PTMi

Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ8CCI5.
MaxQBiQ8CCI5.
PaxDbiQ8CCI5.
PRIDEiQ8CCI5.

PTM databases

iPTMnetiQ8CCI5.
PhosphoSiteiQ8CCI5.

Expressioni

Developmental stagei

At day E9.0, selectively expressed in cells of the developing nervous system and from day E.5 onwards, expressed ubiquitously.1 Publication

Gene expression databases

BgeeiQ8CCI5.
CleanExiMM_RYBP.
GenevisibleiQ8CCI5. MM.

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. Interacts with MDM2, and thereby inhibits ubiquitination of TP53. Identified in a ternary complex containing MDM2, TP53 and RYBP (By similarity). 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. Interacts with PCGF1 (By similarity).By similarity4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
Cbx2P306583EBI-929290,EBI-360174
Ring1O357304EBI-929290,EBI-929310
Rnf2Q9CQJ48EBI-929290,EBI-927321
YY1P254902EBI-929290,EBI-765538From a different organism.

Protein-protein interaction databases

BioGridi207918. 13 interactions.
IntActiQ8CCI5. 14 interactions.
MINTiMINT-4115157.
STRINGi10090.ENSMUSP00000098677.

Structurei

3D structure databases

ProteinModelPortaliQ8CCI5.
SMRiQ8CCI5. Positions 21-60, 145-176.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni143 – 22684Interaction with E4TF1BBy similarityAdd
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 RNF2.1 Publication

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

eggNOGiKOG4477. Eukaryota.
ENOG4111PN1. LUCA.
GeneTreeiENSGT00390000013995.
HOGENOMiHOG000007553.
HOVERGENiHBG001768.
InParanoidiQ8CCI5.
KOiK11469.
OMAiSHISRPK.
OrthoDBiEOG7B8S61.
PhylomeDBiQ8CCI5.
TreeFamiTF350501.

Family and domain databases

InterProiIPR001876. Znf_RanBP2.
[Graphical view]
PfamiPF00641. zf-RanBP. 1 hit.
[Graphical view]
SMARTiSM00547. ZnF_RBZ. 1 hit.
[Graphical view]
SUPFAMiSSF90209. SSF90209. 1 hit.
PROSITEiPS01358. ZF_RANBP2_1. 1 hit.
PS50199. ZF_RANBP2_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8CCI5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTMGDKKSPT RPKRQAKPAA DEGFWDCSVC TFRNSAEAFK CSICDVRKGT
60 70 80 90 100
STRKPRINSQ LVAQQVAQQY ATPPPPKKEK KEKVEKPDKE KPEKDKDISP
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):24,777
Last modified:March 1, 2003 - v1
Checksum:i80E4D647244E213D
GO

Sequence cautioni

The sequence AAD42945.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti143 – 1431T → S in AAD42945 (PubMed:10369680).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK033024 mRNA. Translation: BAC28131.1.
BC053016 mRNA. Translation: AAH53016.1.
BC080287 mRNA. Translation: AAH80287.1.
BC138324 mRNA. Translation: AAI38325.1.
BC138325 mRNA. Translation: AAI38326.1.
AF101779 mRNA. Translation: AAD42945.1. Different initiation.
CCDSiCCDS39579.1.
RefSeqiNP_062717.2. NM_019743.3.
UniGeneiMm.321633.

Genome annotation databases

EnsembliENSMUST00000101118; ENSMUSP00000098677; ENSMUSG00000072872.
GeneIDi56353.
KEGGimmu:56353.
UCSCiuc009dbw.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK033024 mRNA. Translation: BAC28131.1.
BC053016 mRNA. Translation: AAH53016.1.
BC080287 mRNA. Translation: AAH80287.1.
BC138324 mRNA. Translation: AAI38325.1.
BC138325 mRNA. Translation: AAI38326.1.
AF101779 mRNA. Translation: AAD42945.1. Different initiation.
CCDSiCCDS39579.1.
RefSeqiNP_062717.2. NM_019743.3.
UniGeneiMm.321633.

3D structure databases

ProteinModelPortaliQ8CCI5.
SMRiQ8CCI5. Positions 21-60, 145-176.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi207918. 13 interactions.
IntActiQ8CCI5. 14 interactions.
MINTiMINT-4115157.
STRINGi10090.ENSMUSP00000098677.

PTM databases

iPTMnetiQ8CCI5.
PhosphoSiteiQ8CCI5.

Proteomic databases

EPDiQ8CCI5.
MaxQBiQ8CCI5.
PaxDbiQ8CCI5.
PRIDEiQ8CCI5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000101118; ENSMUSP00000098677; ENSMUSG00000072872.
GeneIDi56353.
KEGGimmu:56353.
UCSCiuc009dbw.1. mouse.

Organism-specific databases

CTDi23429.
MGIiMGI:1929059. Rybp.

Phylogenomic databases

eggNOGiKOG4477. Eukaryota.
ENOG4111PN1. LUCA.
GeneTreeiENSGT00390000013995.
HOGENOMiHOG000007553.
HOVERGENiHBG001768.
InParanoidiQ8CCI5.
KOiK11469.
OMAiSHISRPK.
OrthoDBiEOG7B8S61.
PhylomeDBiQ8CCI5.
TreeFamiTF350501.

Miscellaneous databases

ChiTaRSiRybp. mouse.
NextBioi312358.
PROiQ8CCI5.
SOURCEiSearch...

Gene expression databases

BgeeiQ8CCI5.
CleanExiMM_RYBP.
GenevisibleiQ8CCI5. MM.

Family and domain databases

InterProiIPR001876. Znf_RanBP2.
[Graphical view]
PfamiPF00641. zf-RanBP. 1 hit.
[Graphical view]
SMARTiSM00547. ZnF_RBZ. 1 hit.
[Graphical view]
SUPFAMiSSF90209. SSF90209. 1 hit.
PROSITEiPS01358. ZF_RANBP2_1. 1 hit.
PS50199. ZF_RANBP2_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Embryonic gonad.
  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].
    Strain: C57BL/6J.
    Tissue: Brain.
  3. "RYBP, a new repressor protein that interacts with components of the mammalian Polycomb complex, and with the transcription factor YY1."
    Garcia E., Marcos-Gutierrez C., del Mar Lorente M., Moreno J.C., Vidal M.
    EMBO J. 18:3404-3418(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 2-228, INTERACTION WITH YAF2; YY1; CBX2; RING1 AND RNF2.
    Strain: C57BL/10.
  4. "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: DEVELOPMENTAL STAGE.
  5. "Rybp/DEDAF is required for early postimplantation and for central nervous system development."
    Pirity M.K., Locker J., Schreiber-Agus N.
    Mol. Cell. Biol. 25:7193-7202(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISRUPTION PHENOTYPE.
  6. "The Polycomb-associated protein Rybp is a ubiquitin binding protein."
    Arrigoni R., Alam S.L., Wamstad J.A., Bardwell V.J., Sundquist W.I., Schreiber-Agus N.
    FEBS Lett. 580:6233-6241(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBUNIT, INTERACTION WITH RING1 AND RNF2, SUBCELLULAR LOCATION, MUTAGENESIS OF 31-THR-PHE-32, UBIQUITINATION.
  7. "Rybp interacts with Hippi and enhances Hippi-mediated apoptosis."
    Stanton S.E., Blanck J.K., Locker J., Schreiber-Agus N.
    Apoptosis 12:2197-2206(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH IFT57, FUNCTION.
  8. "The transcriptional repressor RYBP is a natively unfolded protein which folds upon binding to DNA."
    Neira J.L., Roman-Trufero M., Contreras L.M., Prieto J., Singh G., Barrera F.N., Renart M.L., Vidal M.
    Biochemistry 48:1348-1360(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RNF2, SUBUNIT, DOMAIN, DNA-BINDING, CIRCULAR DICHROISM.
  9. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-123; SER-127 AND SER-130, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain, Kidney, Lung, Spleen and Testis.

Entry informationi

Entry nameiRYBP_MOUSE
AccessioniPrimary (citable) accession number: Q8CCI5
Secondary accession number(s): B2RRB6, Q9WVK2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 10, 2005
Last sequence update: March 1, 2003
Last modified: March 16, 2016
This is version 114 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.