Q8N488 (RYBP_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	RYBP
Synonyms:	DEDAF, YEAF1

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	228 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.1 Ref.2 Ref.3 Ref.9
Subunit structure	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. Ref.1 Ref.2 Ref.3 Ref.6 Ref.9 Ref.12
Subcellular location	Nucleus. Cytoplasm. Nucleus › nucleoplasm By similarity. Note: Primarily found in the nucleus. Detected in a punctate pattern likely to represent Polycomb group (PcG) bodies By similarity. Ref.1 Ref.2 Ref.3
Tissue specificity	Widely expressed with highest levels in lymphoid tissues and placenta. Ref.1 Ref.2 Ref.3
Domain	Intrinsically unstructured in the absence of binding partners. Folds upon binding to DNA or RNF2 By similarity.
Post-translational modification	Monoubiquitinated By similarity.
Sequence similarities	Contains 1 RanBP2-type zinc finger.
Sequence caution	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.

Ontologies

Keywords
Biological process	Apoptosis Transcription Transcription regulation
Cellular component	Cytoplasm Nucleus
Domain	Zinc-finger
Ligand	DNA-binding Metal-binding Zinc
Molecular function	Repressor
PTM	Phosphoprotein Ubl conjugation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	apoptotic process Inferred from electronic annotation. Source: UniProtKB-KW histone H2A monoubiquitination Inferred from direct assay Ref.6. Source: UniProtKB multicellular organismal development Traceable author statement. Source: ProtInc negative regulation of transcription from RNA polymerase II promoter Traceable author statement. Source: ProtInc transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell nucleoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction Ref.12. Source: UniProtKB transcription corepressor activity Traceable author statement. Source: ProtInc zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
RING1	Q06587	2	EBI-752324,EBI-752313

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 228

228

RING1 and YY1-binding protein

PRO_0000097550

Regions

Zinc finger

21 – 50

30

RanBP2-type

Region

143 – 226

84

Interaction with E4TF1B

Compositional bias

73 – 76

4

Poly-Pro

Compositional bias

77 – 119

43

Lys-rich

Compositional bias

179 – 214

36

Ser-rich

Amino acid modifications

Modified residue

99

1

Phosphoserine Ref.8

Modified residue

127

1

Phosphoserine Ref.7 Ref.8 Ref.11

Modified residue

130

1

Phosphoserine Ref.7 Ref.11

Modified residue

227

1

Phosphoserine Ref.11

Experimental info

Sequence conflict

20

1

A → T in AAH36459. Ref.5

Secondary structure

1

.

.

.

.

.

228

Helix Strand Turn

Details...

Beta strand

149 – 162

14

Beta strand

166 – 175

10

Sequences

	Sequence		Length	Mass (Da)
	Q8N488 [UniParc]. Last modified May 10, 2005. Version 2. Checksum: EB9593460A3F0F4C	FASTA	228	24,822
	10 20 30 40 50 60 MTMGDKKSPT RPKRQAKPAA DEGFWDCSVC TFRNSAEAFK CSICDVRKGT STRKPRINSQ 70 80 90 100 110 120 LVAQQVAQQY ATPPPPKKEK KEKVEKQDKE KPEKDKEISP SVTKKNTNKK TKPKSDILKD 130 140 150 160 170 180 PPSEANSIQS ANATTKTSET NHTSRPRLKN VDRSTAQQLA VTVGNVTVII TDFKEKTRSS 190 200 210 220 STSSSTVTSS AGSEQQNQSS SGSESTDKGS SRSSTPKGDM SAVNDESF

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 11395500] [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: 11953439] [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: 14765135] [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: 15489334] [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: 16943429] [Abstract] Cited for: INTERACTION WITH BCOR; PCGF1; RING1 AND RNF2.
[7]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed: 18669648] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-127 AND SER-130, MASS SPECTROMETRY. 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: 19413330] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-99 AND SER-127, MASS SPECTROMETRY. Tissue: Embryonic kidney.
[9]	"RYBP stabilizes p53 by modulating MDM2." Chen D., Zhang J., Li M., Rayburn E.R., Wang H., Zhang R. EMBO Rep. 10:166-172(2009) [PubMed: 19098711] [Abstract] Cited for: FUNCTION, INTERACTION WITH MDM2, IDENTIFICATION IN A COMPLEX WITH MDM2 AND TP53.
[10]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed: 21269460] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[11]	"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: 19690332] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-127; SER-130 AND SER-227, MASS SPECTROMETRY. Tissue: Leukemic T-cell.
[12]	"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: 20696397] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 145-179 IN COMPLEX WITH RNF2/RING1B, INTERACTION WITH RNF2.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

IPI

IPI00296594.

RefSeq

NP_036366.3. NM_012234.5.

UniGene

Hs.7910.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3IXS	X-ray	1.70	B/D/F/H/J/L	145-179	[»]

ProteinModelPortal

Q8N488.

SMR

Q8N488. Positions 21-60, 145-176.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-41435N.

IntAct

Q8N488. 3 interactions.

MINT

MINT-158357.

STRING

Q8N488.

PTM databases

PhosphoSite

Q8N488.

Polymorphism databases

DMDM

78102506.

Proteomic databases

PRIDE

Q8N488.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000477973; ENSP00000419494; ENSG00000163602.

GeneID

23429.

KEGG

hsa:23429.

UCSC

uc003dpe.1. human.

Organism-specific databases

CTD

23429.

GeneCards

GC03M072506.

H-InvDB

HIX0003460.

HGNC

HGNC:10480. RYBP.

MIM

607535. gene.

neXtProt

NX_Q8N488.

PharmGKB

PA34893.

GenAtlas

Search...

Phylogenomic databases

eggNOG

prNOG20187.

GeneTree

ENSGT00390000013995.

HOGENOM

HBG713531.

HOVERGEN

HBG001768.

InParanoid

Q8N488.

OrthoDB

EOG4F4SCG.

Gene expression databases

ArrayExpress

Q8N488.

Bgee

Q8N488.

CleanEx

HS_RYBP.

Genevestigator

Q8N488.

GermOnline

ENSG00000163602. Homo sapiens.

Family and domain databases

InterPro

IPR001876. Znf_RanBP2.
[Graphical view]

KO

K11469.

Pfam

PF00641. zf-RanBP. 1 hit.
[Graphical view]

SMART

SM00547. ZnF_RBZ. 1 hit.
[Graphical view]

PROSITE

PS01358. ZF_RANBP2_1. 1 hit.
PS50199. ZF_RANBP2_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

45669.

SOURCE

Search...

Entry information

Entry name

RYBP_HUMAN

Accession

Primary (citable) accession number: Q8N488
Secondary accession number(s): Q9P2W5, Q9UMW4

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 10, 2005
Last sequence update:	May 10, 2005
Last modified:	January 25, 2012
This is version 84 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.