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Protein

RING1 and YY1-binding protein

Gene

RYBP

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1-like complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A 'Lys-119', rendering chromatin heritably changed in its expressibility (PubMed:25519132). Component of a PRC1-like complex that mediates monoubiquitination of histone H2A 'Lys-119' on the X chromosome and is required for normal silencing of one copy of the X chromosome in XX females. May stimulate ubiquitination of histone H2A 'Lys-119' by recruiting the complex to target sites (By similarity). Inhibits ubiquitination and subsequent degradation of TP53, and thereby plays a role in regulating transcription of TP53 target genes (PubMed:19098711). May also regulate the ubiquitin-mediated proteasomal degradation of other proteins like FANK1 to regulate apoptosis (PubMed:14765135, PubMed:27060496). May be implicated in the regulation of the transcription as a repressor of the transcriptional activity of E4TF1 (PubMed:11953439). May bind to DNA (By similarity).By similarity4 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri21 – 50RanBP2-typePROSITE-ProRule annotationAdd BLAST30

GO - Molecular functioni

  • DNA binding Source: UniProtKB-KW
  • metal ion binding Source: UniProtKB-KW
  • transcription corepressor activity Source: ProtInc

GO - Biological processi

  • apoptotic process Source: UniProtKB-KW
  • histone H2A monoubiquitination Source: UniProtKB
  • multicellular organism development Source: ProtInc
  • negative regulation of proteasomal ubiquitin-dependent protein catabolic process Source: UniProtKB
  • negative regulation of transcription from RNA polymerase II promoter Source: Ensembl
  • positive regulation of apoptotic process Source: UniProtKB
  • positive regulation of transcription, DNA-templated Source: UniProtKB
  • transcription, DNA-templated Source: UniProtKB-KW

Keywordsi

Molecular functionDNA-binding, Repressor
Biological processApoptosis, Transcription, Transcription regulation
LigandMetal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-8939243. RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known.
R-HSA-8953750. Transcriptional Regulation by E2F6.
SignaLinkiQ8N488.
SIGNORiQ8N488.

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
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

EuPathDBiHostDB:ENSG00000163602.9.
HGNCiHGNC:10480. RYBP.

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi23429.
PharmGKBiPA34893.

Polymorphism and mutation databases

BioMutaiRYBP.
DMDMi78102506.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000975501 – 228RING1 and YY1-binding proteinAdd BLAST228

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki77Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei99PhosphoserineCombined sources1
Modified residuei123PhosphoserineCombined sources1
Modified residuei127PhosphoserineCombined sources1
Modified residuei130PhosphoserineCombined sources1
Modified residuei227PhosphoserineCombined sources1

Post-translational modificationi

Monoubiquitinated.By similarity

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ8N488.
MaxQBiQ8N488.
PaxDbiQ8N488.
PeptideAtlasiQ8N488.
PRIDEiQ8N488.

PTM databases

iPTMnetiQ8N488.
PhosphoSitePlusiQ8N488.

Expressioni

Tissue specificityi

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

Gene expression databases

BgeeiENSG00000163602.
CleanExiHS_RYBP.
GenevisibleiQ8N488. HS.

Organism-specific databases

HPAiHPA053357.

Interactioni

Subunit structurei

Monomer. Component of repressive BCOR complex containing Polycomb group subcomplex at least composed of BCOR, PCGF1, RING1 and RNF2/RING2 (PubMed:16943429). Component of PCR1-like complexes (PubMed:26687479, PubMed:20696397). Interacts with PCGF1 (PubMed:26687479). Part of a PCR1-like complex that contains AUTS2, PCGF5, RNF2, CSNK2B AND RYBP (PubMed:25519132). Interacts with RNF2; the interaction is direct (PubMed:20696397). Interacts with CBX2, YAF2, RING1 and RNF2 (By similarity). Interacts with ubiquitin and ubiquitinated proteins (By similarity). Interacts with ubiquitinated histone H2A (By similarity). Interacts with apoptin, DEDD, FADD, CASP8, CASP10, YY1 and GABPB1 (PubMed:11395500, PubMed:11953439, PubMed:14765135). Together with GABPB1 and YY1, it forms a ternary complex, probably being the bridge factor between these two transcription factors (PubMed:11953439). Interacts with MDM2, and thereby inhibits ubiquitination of TP53 (PubMed:19098711). Identified in a ternary complex containing MDM2, TP53 and RYBP (PubMed:19098711). Interacts with FANK1; may prevent the ubiquitin-mediated proteasomal degradation of FANK1 (PubMed:27060496). Interacts with IFT57 (By similarity).By similarity9 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi116997. 58 interactors.
CORUMiQ8N488.
DIPiDIP-41435N.
IntActiQ8N488. 39 interactors.
MINTiMINT-158357.
STRINGi9606.ENSP00000419494.

Structurei

Secondary structure

1228
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi149 – 163Combined sources15
Beta strandi166 – 175Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3IXSX-ray1.70B/D/F/H/J/L145-179[»]
DisProtiDP00694.
ProteinModelPortaliQ8N488.
SMRiQ8N488.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8N488.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni143 – 226Interaction with GABPB1 and FANK12 PublicationsAdd BLAST84

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi73 – 76Poly-Pro4
Compositional biasi77 – 119Lys-richAdd BLAST43
Compositional biasi179 – 214Ser-richAdd BLAST36

Domaini

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

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri21 – 50RanBP2-typePROSITE-ProRule annotationAdd BLAST30

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG4477. Eukaryota.
ENOG4111PN1. LUCA.
HOVERGENiHBG001768.
InParanoidiQ8N488.
KOiK11469.
OrthoDBiEOG091G10HB.
PhylomeDBiQ8N488.
TreeFamiTF350501.

Family and domain databases

InterProiView protein in InterPro
IPR033774. YAF2_RYBP.
IPR001876. Znf_RanBP2.
IPR036443. Znf_RanBP2_sf.
PfamiView protein in Pfam
PF17219. YAF2_RYBP. 1 hit.
PF00641. zf-RanBP. 1 hit.
SMARTiView protein in SMART
SM00547. ZnF_RBZ. 1 hit.
SUPFAMiSSF90209. SSF90209. 1 hit.
PROSITEiView protein in PROSITE
PS01358. ZF_RANBP2_1. 1 hit.
PS50199. ZF_RANBP2_2. 1 hit.

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

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti20A → T in AAH36459 (PubMed:15489334).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.4. human.

Similar proteinsi

Entry informationi

Entry nameiRYBP_HUMAN
AccessioniPrimary (citable) accession number: Q8N488
Secondary accession number(s): Q9P2W5, Q9UMW4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 10, 2005
Last sequence update: May 10, 2005
Last modified: November 22, 2017
This is version 140 of the entry and version 2 of the sequence. See 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