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Protein

Histone-binding protein RBBP4

Gene

Rbbp4

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA. Component of several complexes which regulate chromatin metabolism. These include the chromatin assembly factor 1 (CAF-1) complex, which is required for chromatin assembly following DNA replication and DNA repair; the core histone deacetylase (HDAC) complex, which promotes histone deacetylation and consequent transcriptional repression; the nucleosome remodeling and histone deacetylase complex (the NuRD complex), which promotes transcriptional repression by histone deacetylation and nucleosome remodeling; and the PRC2/EED-EZH2 complex, which promotes repression of homeotic genes during development; and the NURF (nucleosome remodeling factor) complex (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Repressor

Keywords - Biological processi

Cell cycle, DNA replication, Transcription, Transcription regulation

Enzyme and pathway databases

ReactomeiR-MMU-1538133. G0 and Early G1.
R-MMU-212300. PRC2 methylates histones and DNA.
R-MMU-2559580. Oxidative Stress Induced Senescence.
R-MMU-3214841. PKMTs methylate histone lysines.
R-MMU-573389. NoRC negatively regulates rRNA expression.
R-MMU-606279. Deposition of new CENPA-containing nucleosomes at the centromere.
R-MMU-73762. RNA Polymerase I Transcription Initiation.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone-binding protein RBBP4
Alternative name(s):
Chromatin assembly factor 1 subunit C
Short name:
CAF-1 subunit C
Chromatin assembly factor I p48 subunit
Short name:
CAF-I 48 kDa subunit
Short name:
CAF-I p48
Nucleosome-remodeling factor subunit RBAP48
Retinoblastoma-binding protein 4
Short name:
RBBP-4
Retinoblastoma-binding protein p48
Gene namesi
Name:Rbbp4
Synonyms:Rbap48
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 4

Organism-specific databases

MGIiMGI:1194912. Rbbp4.

Subcellular locationi

GO - Cellular componenti

  • CAF-1 complex Source: UniProtKB
  • ESC/E(Z) complex Source: UniProtKB
  • nuclear chromatin Source: MGI
  • nucleoplasm Source: MGI
  • nucleus Source: HGNC
  • NuRD complex Source: MGI
  • NURF complex Source: MGI
  • protein complex Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedCombined sources
Chaini2 – 425424Histone-binding protein RBBP4PRO_0000051187Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanineCombined sources
Modified residuei4 – 41N6-acetyllysine; alternateBy similarity
Cross-linki4 – 4Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternateBy similarity
Modified residuei110 – 1101PhosphoserineBy similarity
Modified residuei160 – 1601N6-acetyllysine; alternateCombined sources
Cross-linki160 – 160Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateBy similarity

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ60972.
MaxQBiQ60972.
PaxDbiQ60972.
PRIDEiQ60972.

2D gel databases

REPRODUCTION-2DPAGEQ60972.

PTM databases

iPTMnetiQ60972.
PhosphoSiteiQ60972.
SwissPalmiQ60972.

Expressioni

Tissue specificityi

Higher levels in brain, thymus, lung, spleen, kidney, testis, and ovary/uterus; lower levels in heart, liver, and muscle.1 Publication

Gene expression databases

BgeeiQ60972.
CleanExiMM_RBBP4.
ExpressionAtlasiQ60972. baseline and differential.
GenevisibleiQ60972. MM.

Interactioni

Subunit structurei

Binds directly to helix 1 of the histone fold of histone H4, a region that is not accessible when H4 is in chromatin. Subunit of the chromatin assembly factor 1 (CAF-1) complex, which is composed of RBBP4, CHAF1B and CHAF1A. Subunit of the core histone deacetylase (HDAC) complex, which is composed of HDAC1, HDAC2, RBBP4 and RBBP7. The core HDAC complex associates with SIN3A, ARID4B/SAP180, SAP18, SAP30, SAP130, SUDS3/SAP45 and possibly ARID4A/RBP1 and ING1 to form the SIN3 HDAC complex. The core HDAC complex may also associate with MTA2, MBD3, CHD3 and CHD4 to form the nucleosome remodeling and histone deacetylase complex (the NuRD complex). The NuRD complex may also interact with MBD3L1 and MBD3L2. Component of the PRC2/EED-EZH1 complex, which includes EED, EZH1, SUZ12, RBBP4 and AEBP2. Interacts with MTA1. Subunit of the PRC2/EED-EZH2 complex, which is composed of at least EED, EZH2, RBBP4, RBBP7 and SUZ12. The PRC2/EED-EZH2 complex may also associate with HDAC1. Component of the PRC2/EED-EZH1 complex, which includes EED, EZH1, SUZ12, RBBP4 and AEBP2. Part of the nucleosome remodeling factor (NURF) complex which consists of SMARCA1; BPTF; RBBP4 and RBBP7. Interacts with the viral protein-binding domain of the retinoblastoma protein (RB1). Interacts with SPEN/MINT. Interacts with BRCA1 (By similarity). Interacts with CREBBP, and this interaction may be enhanced by the binding of phosphorylated CREB1 to CREBBP. Interacts with SAP30, SUV39H1 and HDAC7. Component of the DREAM complex (also named LINC complex) at least composed of E2F4, E2F5, LIN9, LIN37, LIN52, LIN54, MYBL1, MYBL2, RBL1, RBL2, RBBP4, TFDP1 and TFDP2. The complex exists in quiescent cells where it represses cell cycle-dependent genes. It dissociates in S phase when LIN9, LIN37, LIN52 and LIN54 form a subcomplex that binds to MYBL2.By similarity5 Publications

GO - Molecular functioni

Protein-protein interaction databases

BioGridi202816. 19 interactions.
DIPiDIP-32855N.
IntActiQ60972. 16 interactions.
MINTiMINT-4131905.
STRINGi10090.ENSMUSP00000099658.

Structurei

3D structure databases

ProteinModelPortaliQ60972.
SMRiQ60972. Positions 7-410.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati122 – 15534WD 1Add
BLAST
Repeati175 – 20632WD 2Add
BLAST
Repeati225 – 25632WD 3Add
BLAST
Repeati271 – 30232WD 4Add
BLAST
Repeati315 – 34632WD 5Add
BLAST
Repeati372 – 40332WD 6Add
BLAST

Sequence similaritiesi

Contains 6 WD repeats.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, WD repeat

Phylogenomic databases

eggNOGiKOG0264. Eukaryota.
ENOG410XNU9. LUCA.
GeneTreeiENSGT00570000079069.
HOGENOMiHOG000160330.
HOVERGENiHBG053236.
InParanoidiQ60972.
KOiK10752.
OMAiTRCNNTS.
OrthoDBiEOG70PBXB.
TreeFamiTF106485.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
InterProiIPR020472. G-protein_beta_WD-40_rep.
IPR022052. Histone-bd_RBBP4_N.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR019775. WD40_repeat_CS.
IPR017986. WD40_repeat_dom.
[Graphical view]
PfamiPF12265. CAF1C_H4-bd. 1 hit.
PF00400. WD40. 5 hits.
[Graphical view]
PRINTSiPR00320. GPROTEINBRPT.
SMARTiSM00320. WD40. 6 hits.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 1 hit.
PROSITEiPS00678. WD_REPEATS_1. 3 hits.
PS50082. WD_REPEATS_2. 5 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q60972-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MADKEAAFDD AVEERVINEE YKIWKKNTPF LYDLVMTHAL EWPSLTAQWL
60 70 80 90 100
PDVTRPEGKD FSIHRLVLGT HTSDEQNHLV IASVQLPNDD AQFDASHYDS
110 120 130 140 150
EKGEFGGFGS VSGKIEIEIK INHEGEVNRA RYMPQNPCII ATKTPSSDVL
160 170 180 190 200
VFDYTKHPSK PDPSGECNPD LRLRGHQKEG YGLSWNPNLS GHLLSASDDH
210 220 230 240 250
TICLWDISAV PKEGKVVDAK TIFTGHTAVV EDVSWHLLHE SLFGSVADDQ
260 270 280 290 300
KLMIWDTRSN NTSKPSHSVD AHTAEVNCLS FNPYSEFILA TGSADKTVAL
310 320 330 340 350
WDLRNLKLKL HSFESHKDEI FQVQWSPHNE TILASSGTDR RLNVWDLSKI
360 370 380 390 400
GEEQSPEDAE DGPPELLFIH GGHTAKISDF SWNPNEPWVI CSVSEDNIMQ
410 420
VWQMAENIYN DEDPEGSVDP EGQGS
Length:425
Mass (Da):47,656
Last modified:July 27, 2011 - v5
Checksum:iB71E2D55A444C360
GO

Sequence cautioni

The sequence AAC52275.1 differs from that shown. Reason: Frameshift at position 425. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti213 – 2131E → K in AAC52275 (PubMed:7503932).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U35141 mRNA. Translation: AAC52275.1. Frameshift.
AL607123 Genomic DNA. Translation: CAM22958.1.
CU234133 Genomic DNA. Translation: CAQ52144.1.
CH466552 Genomic DNA. Translation: EDL30202.1.
BC138568 mRNA. Translation: AAI38569.1.
BC138570 mRNA. Translation: AAI38571.1.
CCDSiCCDS18688.1.
PIRiI49366.
RefSeqiNP_033056.2. NM_009030.3.
UniGeneiMm.12145.

Genome annotation databases

EnsembliENSMUST00000102598; ENSMUSP00000099658; ENSMUSG00000057236.
GeneIDi19646.
KEGGimmu:19646.
UCSCiuc008uwt.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U35141 mRNA. Translation: AAC52275.1. Frameshift.
AL607123 Genomic DNA. Translation: CAM22958.1.
CU234133 Genomic DNA. Translation: CAQ52144.1.
CH466552 Genomic DNA. Translation: EDL30202.1.
BC138568 mRNA. Translation: AAI38569.1.
BC138570 mRNA. Translation: AAI38571.1.
CCDSiCCDS18688.1.
PIRiI49366.
RefSeqiNP_033056.2. NM_009030.3.
UniGeneiMm.12145.

3D structure databases

ProteinModelPortaliQ60972.
SMRiQ60972. Positions 7-410.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi202816. 19 interactions.
DIPiDIP-32855N.
IntActiQ60972. 16 interactions.
MINTiMINT-4131905.
STRINGi10090.ENSMUSP00000099658.

PTM databases

iPTMnetiQ60972.
PhosphoSiteiQ60972.
SwissPalmiQ60972.

2D gel databases

REPRODUCTION-2DPAGEQ60972.

Proteomic databases

EPDiQ60972.
MaxQBiQ60972.
PaxDbiQ60972.
PRIDEiQ60972.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000102598; ENSMUSP00000099658; ENSMUSG00000057236.
GeneIDi19646.
KEGGimmu:19646.
UCSCiuc008uwt.1. mouse.

Organism-specific databases

CTDi5928.
MGIiMGI:1194912. Rbbp4.

Phylogenomic databases

eggNOGiKOG0264. Eukaryota.
ENOG410XNU9. LUCA.
GeneTreeiENSGT00570000079069.
HOGENOMiHOG000160330.
HOVERGENiHBG053236.
InParanoidiQ60972.
KOiK10752.
OMAiTRCNNTS.
OrthoDBiEOG70PBXB.
TreeFamiTF106485.

Enzyme and pathway databases

ReactomeiR-MMU-1538133. G0 and Early G1.
R-MMU-212300. PRC2 methylates histones and DNA.
R-MMU-2559580. Oxidative Stress Induced Senescence.
R-MMU-3214841. PKMTs methylate histone lysines.
R-MMU-573389. NoRC negatively regulates rRNA expression.
R-MMU-606279. Deposition of new CENPA-containing nucleosomes at the centromere.
R-MMU-73762. RNA Polymerase I Transcription Initiation.

Miscellaneous databases

ChiTaRSiRbbp4. mouse.
NextBioi296894.
PROiQ60972.
SOURCEiSearch...

Gene expression databases

BgeeiQ60972.
CleanExiMM_RBBP4.
ExpressionAtlasiQ60972. baseline and differential.
GenevisibleiQ60972. MM.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
InterProiIPR020472. G-protein_beta_WD-40_rep.
IPR022052. Histone-bd_RBBP4_N.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR019775. WD40_repeat_CS.
IPR017986. WD40_repeat_dom.
[Graphical view]
PfamiPF12265. CAF1C_H4-bd. 1 hit.
PF00400. WD40. 5 hits.
[Graphical view]
PRINTSiPR00320. GPROTEINBRPT.
SMARTiSM00320. WD40. 6 hits.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 1 hit.
PROSITEiPS00678. WD_REPEATS_1. 3 hits.
PS50082. WD_REPEATS_2. 5 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Dual retinoblastoma-binding proteins with properties related to a negative regulator of ras in yeast."
    Qian Y.-W., Lee E.Y.-H.P.
    J. Biol. Chem. 270:25507-25513(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  3. Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
    Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "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.
  5. "SAP30, a component of the mSin3 corepressor complex involved in N-CoR-mediated repression by specific transcription factors."
    Laherty C.D., Billin A.N., Lavinsky R.M., Yochum G.S., Bush A.C., Sun J.-M., Mullen T.-M., Davie J.R., Rose D.W., Glass C.K., Rosenfeld M.G., Ayer D.E., Eisenman R.N.
    Mol. Cell 2:33-42(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH SAP30.
  6. "Histone binding protein RbAp48 interacts with a complex of CREB binding protein and phosphorylated CREB."
    Zhang Q., Vo N., Goodman R.H.
    Mol. Cell. Biol. 20:4970-4978(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH CREBBP.
  7. Cited for: INTERACTION WITH HDAC7.
  8. "Functional and physical interaction between the histone methyl transferase Suv39H1 and histone deacetylases."
    Vaute O., Nicolas E., Vandel L., Trouche D.
    Nucleic Acids Res. 30:475-481(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH SUV39H1.
  9. "Comprehensive identification of phosphorylation sites in postsynaptic density preparations."
    Trinidad J.C., Specht C.G., Thalhammer A., Schoepfer R., Burlingame A.L.
    Mol. Cell. Proteomics 5:914-922(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS], IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain.
  10. "EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency."
    Shen X., Liu Y., Hsu Y.-J., Fujiwara Y., Kim J., Mao X., Yuan G.-C., Orkin S.H.
    Mol. Cell 32:491-502(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE PRC2/EED-EZH1 COMPLEX.
  11. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain, Brown adipose tissue, Heart, Kidney, Liver, Lung, Spleen and Testis.
  12. "SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways."
    Park J., Chen Y., Tishkoff D.X., Peng C., Tan M., Dai L., Xie Z., Zhang Y., Zwaans B.M., Skinner M.E., Lombard D.B., Zhao Y.
    Mol. Cell 50:919-930(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-160, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Embryonic fibroblast.

Entry informationi

Entry nameiRBBP4_MOUSE
AccessioniPrimary (citable) accession number: Q60972
Secondary accession number(s): A2A875
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: July 27, 2011
Last modified: May 11, 2016
This is version 151 of the entry and version 5 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.