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Protein

Transcriptional repressor protein YY1

Gene

YY1

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

Functioni

Multifunctional transcription factor that exhibits positive and negative control on a large number of cellular and viral genes by binding to sites overlapping the transcription start site. Binds to the consensus sequence 5'-CCGCCATNTT-3'; some genes have been shown to contain a longer binding motif allowing enhanced binding; the initial CG dinucleotide can be methylated greatly reducing the binding affinity. The effect on transcription regulation is depending upon the context in which it binds and diverse mechanisms of action include direct activation or repression, indirect activation or repression via cofactor recruitment, or activation or repression by disruption of binding sites or conformational DNA changes. Its activity is regulated by transcription factors and cytoplasmic proteins that have been shown to abrogate or completely inhibit YY1-mediated activation or repression. For example, it acts as a repressor in absence of adenovirus E1A protein but as an activator in its presence. Acts synergistically with the SMAD1 and SMAD4 in bone morphogenetic protein (BMP)-mediated cardiac-specific gene expression (PubMed:15329343). Binds to SMAD binding elements (SBEs) (5'-GTCT/AGAC-3') within BMP response element (BMPRE) of cardiac activating regions. May play an important role in development and differentiation. Proposed to recruit the PRC2/EED-EZH2 complex to target genes that are transcriptional repressed. Involved in DNA repair. In vitro, binds to DNA recombination intermediate structures (Holliday junctions).3 Publications
Proposed core component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair; proposed to target the INO80 complex to YY1-responsive elements.2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi298Zinc 11
Metal bindingi303Zinc 11
Metal bindingi316Zinc 11
Metal bindingi320Zinc 11
Metal bindingi327Zinc 21
Metal bindingi330Zinc 21
Metal bindingi343Zinc 21
Metal bindingi347Zinc 21
Metal bindingi355Zinc 31
Metal bindingi360Zinc 31
Metal bindingi373Zinc 31
Metal bindingi377Zinc 31
Metal bindingi385Zinc 41
Metal bindingi390Zinc 41
Metal bindingi403Zinc 41
Metal bindingi407Zinc 41

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri296 – 320C2H2-type 1PROSITE-ProRule annotationAdd BLAST25
Zinc fingeri325 – 347C2H2-type 2PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri353 – 377C2H2-type 3PROSITE-ProRule annotationAdd BLAST25
Zinc fingeri383 – 407C2H2-type 4PROSITE-ProRule annotationAdd BLAST25

GO - Molecular functioni

  • DNA binding Source: MGI
  • enhancer sequence-specific DNA binding Source: AgBase
  • four-way junction DNA binding Source: UniProtKB
  • RNA binding Source: MGI
  • SMAD binding Source: AgBase
  • transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding Source: BHF-UCL
  • transcription coactivator activity Source: ProtInc
  • transcription corepressor activity Source: ProtInc
  • transcription factor activity, sequence-specific DNA binding Source: ProtInc
  • transcription regulatory region DNA binding Source: MGI
  • zinc ion binding Source: ProtInc

GO - Biological processi

  • cell differentiation Source: UniProtKB-KW
  • cellular response to DNA damage stimulus Source: UniProtKB
  • cellular response to UV Source: UniProtKB
  • double-strand break repair via homologous recombination Source: UniProtKB
  • negative regulation of gene expression Source: CACAO
  • negative regulation of transcription from RNA polymerase II promoter Source: MGI
  • regulation of transcription from RNA polymerase II promoter Source: ProtInc
  • response to UV-C Source: UniProtKB
  • spermatogenesis Source: UniProtKB-KW
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Activator, Repressor

Keywords - Biological processi

Differentiation, DNA damage, DNA recombination, DNA repair, Spermatogenesis, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciZFISH:ENSG00000100811-MONOMER.
ReactomeiR-HSA-5617472. Activation of anterior HOX genes in hindbrain development during early embryogenesis.
R-HSA-5689603. UCH proteinases.
R-HSA-5696394. DNA Damage Recognition in GG-NER.
R-HSA-8866910. TFAP2 (AP-2) family regulates transcription of growth factors and their receptors.
SignaLinkiP25490.
SIGNORiP25490.

Names & Taxonomyi

Protein namesi
Recommended name:
Transcriptional repressor protein YY1
Alternative name(s):
Delta transcription factor
INO80 complex subunit S
NF-E1
Yin and yang 1
Short name:
YY-1
Gene namesi
Name:YY1
Synonyms:INO80S
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 14

Organism-specific databases

HGNCiHGNC:12856. YY1.

Subcellular locationi

GO - Cellular componenti

  • Ino80 complex Source: UniProtKB
  • nuclear matrix Source: UniProtKB-SubCell
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi7528.
OpenTargetsiENSG00000100811.
PharmGKBiPA37445.

Polymorphism and mutation databases

DMDMi3915889.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000471901 – 414Transcriptional repressor protein YY1Add BLAST414

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei118PhosphoserineCombined sources1
Cross-linki183Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei187PhosphoserineCombined sources1
Modified residuei247PhosphoserineCombined sources1
Cross-linki286Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki288Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei378PhosphothreonineCombined sources1

Post-translational modificationi

Transiently poly-ADP-ribosylated by PARP1 upon DNA damage, with the effect of decreasing affinity of YY1 to its cognate DNA binding sites.
Ubiquitinated.1 Publication

Keywords - PTMi

ADP-ribosylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiP25490.
MaxQBiP25490.
PaxDbiP25490.
PeptideAtlasiP25490.
PRIDEiP25490.

PTM databases

iPTMnetiP25490.
PhosphoSitePlusiP25490.

Miscellaneous databases

PMAP-CutDBP25490.

Expressioni

Gene expression databases

BgeeiENSG00000100811.
CleanExiHS_YY1.
ExpressionAtlasiP25490. baseline and differential.
GenevisibleiP25490. HS.

Organism-specific databases

HPAiCAB009392.
HPA001119.

Interactioni

Subunit structurei

Interacts with YAF2 through the region encompassing the first and second zinc fingers (PubMed:9016636). Component of the chromatin remodeling INO80 complex; specifically part of a complex module associated with the DBINO domain of INO80 (PubMed:17721549, PubMed:18026119, PubMed:18922472, PubMed:21303910). Interacts with EED and EZH2; the interactions are indicative for an association with the PRC2/EED-EZH2 complex (PubMed:11158321). Interacts with SFMBT2 (PubMed:23385818). Found in a complex with SMAD1 and SMAD4 (PubMed:15329343). Found in a complex with YY1, SIN3A and HDAC1 (By similarity).By similarity8 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
P032593EBI-765538,EBI-6947456From a different organism.
ACTL6AO960196EBI-765538,EBI-355018
ARRB1P494074EBI-765538,EBI-743313
E1AQ8JSK44EBI-765538,EBI-7453955From a different organism.
INO80Q9ULG16EBI-765538,EBI-769345
KRTAP9-3Q9BYQ34EBI-765538,EBI-1043191
KRTAP9-8Q9BYQ04EBI-765538,EBI-11958364
PRKDCP785272EBI-765538,EBI-352053
RUVBL1Q9Y2655EBI-765538,EBI-353675
RUVBL2Q9Y2306EBI-765538,EBI-352939
RybpQ8CCI52EBI-765538,EBI-929290From a different organism.

GO - Molecular functioni

  • SMAD binding Source: AgBase

Protein-protein interaction databases

BioGridi113360. 129 interactors.
DIPiDIP-150N.
IntActiP25490. 77 interactors.
MINTiMINT-157439.
STRINGi9606.ENSP00000262238.

Structurei

Secondary structure

1414
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi207 – 211Combined sources5
Beta strandi220 – 224Combined sources5
Beta strandi306 – 309Combined sources4
Helixi310 – 317Combined sources8
Helixi318 – 320Combined sources3
Turni328 – 330Combined sources3
Beta strandi333 – 336Combined sources4
Helixi337 – 343Combined sources7
Helixi344 – 346Combined sources3
Turni358 – 360Combined sources3
Beta strandi363 – 365Combined sources3
Helixi367 – 378Combined sources12
Turni397 – 400Combined sources4
Helixi401 – 407Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1UBDX-ray2.50C291-414[»]
1ZNMNMR-A352-379[»]
4C5IX-ray2.59C199-228[»]
ProteinModelPortaliP25490.
SMRiP25490.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP25490.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 170Interaction with the SMAD1/SMAD4 complexAdd BLAST170
Regioni257 – 341Involved in nuclear matrix associationAdd BLAST85
Regioni295 – 414Binding to DNAAdd BLAST120
Regioni333 – 371Involved in repression of activated transcriptionAdd BLAST39
Regioni371 – 397Involved in masking transactivation domainAdd BLAST27

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi43 – 53Asp/Glu-rich (acidic)Add BLAST11
Compositional biasi54 – 69Gly-richAdd BLAST16
Compositional biasi70 – 80Poly-HisAdd BLAST11
Compositional biasi159 – 170Gly/Ser-richAdd BLAST12

Sequence similaritiesi

Belongs to the YY transcription factor family.Curated
Contains 4 C2H2-type zinc fingers.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri296 – 320C2H2-type 1PROSITE-ProRule annotationAdd BLAST25
Zinc fingeri325 – 347C2H2-type 2PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri353 – 377C2H2-type 3PROSITE-ProRule annotationAdd BLAST25
Zinc fingeri383 – 407C2H2-type 4PROSITE-ProRule annotationAdd BLAST25

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1721. Eukaryota.
COG5048. LUCA.
GeneTreeiENSGT00760000118771.
HOGENOMiHOG000008232.
HOVERGENiHBG006823.
InParanoidiP25490.
KOiK09201.
OMAiGGRKWEQ.
OrthoDBiEOG091G03FM.
PhylomeDBiP25490.
TreeFamiTF106493.

Family and domain databases

Gene3Di3.30.160.60. 4 hits.
InterProiIPR017114. TF_Yin_yang.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
PfamiPF00096. zf-C2H2. 1 hit.
[Graphical view]
PIRSFiPIRSF037113. TF_Yin_yang. 1 hit.
SMARTiSM00355. ZnF_C2H2. 4 hits.
[Graphical view]
PROSITEiPS00028. ZINC_FINGER_C2H2_1. 4 hits.
PS50157. ZINC_FINGER_C2H2_2. 4 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P25490-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MASGDTLYIA TDGSEMPAEI VELHEIEVET IPVETIETTV VGEEEEEDDD
60 70 80 90 100
DEDGGGGDHG GGGGHGHAGH HHHHHHHHHH PPMIALQPLV TDDPTQVHHH
110 120 130 140 150
QEVILVQTRE EVVGGDDSDG LRAEDGFEDQ ILIPVPAPAG GDDDYIEQTL
160 170 180 190 200
VTVAAAGKSG GGGSSSSGGG RVKKGGGKKS GKKSYLSGGA GAAGGGGADP
210 220 230 240 250
GNKKWEQKQV QIKTLEGEFS VTMWSSDEKK DIDHETVVEE QIIGENSPPD
260 270 280 290 300
YSEYMTGKKL PPGGIPGIDL SDPKQLAEFA RMKPRKIKED DAPRTIACPH
310 320 330 340 350
KGCTKMFRDN SAMRKHLHTH GPRVHVCAEC GKAFVESSKL KRHQLVHTGE
360 370 380 390 400
KPFQCTFEGC GKRFSLDFNL RTHVRIHTGD RPYVCPFDGC NKKFAQSTNL
410
KSHILTHAKA KNNQ
Length:414
Mass (Da):44,713
Last modified:December 15, 1998 - v2
Checksum:i058C05A0AD2D04E6
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti65H → R in AAA59926 (PubMed:1946405).Curated1
Sequence conflicti196G → R in AAA59467 (PubMed:1655281).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_074172372T → R Found in patients with late onset insulinomas; alters DNA-binding motif; increases transactivation activity; produces a constitutive activation of cAMP and Ca2+ signaling pathways involved in insulin secretion. 2 PublicationsCorresponds to variant rs386834266dbSNPEnsembl.1
Natural variantiVAR_065086380D → Y De novo variant found in a patient with mental retardation. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M77698 mRNA. Translation: AAA59467.1.
M76541 mRNA. Translation: AAA59926.1.
Z14077 mRNA. Translation: CAA78455.1.
BC037308 mRNA. Translation: AAH37308.1.
BC065366 mRNA. Translation: AAH65366.1.
CCDSiCCDS9957.1.
PIRiA40350.
RefSeqiNP_003394.1. NM_003403.4.
UniGeneiHs.388927.
Hs.603118.

Genome annotation databases

EnsembliENST00000262238; ENSP00000262238; ENSG00000100811.
GeneIDi7528.
KEGGihsa:7528.
UCSCiuc001ygy.3. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M77698 mRNA. Translation: AAA59467.1.
M76541 mRNA. Translation: AAA59926.1.
Z14077 mRNA. Translation: CAA78455.1.
BC037308 mRNA. Translation: AAH37308.1.
BC065366 mRNA. Translation: AAH65366.1.
CCDSiCCDS9957.1.
PIRiA40350.
RefSeqiNP_003394.1. NM_003403.4.
UniGeneiHs.388927.
Hs.603118.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1UBDX-ray2.50C291-414[»]
1ZNMNMR-A352-379[»]
4C5IX-ray2.59C199-228[»]
ProteinModelPortaliP25490.
SMRiP25490.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi113360. 129 interactors.
DIPiDIP-150N.
IntActiP25490. 77 interactors.
MINTiMINT-157439.
STRINGi9606.ENSP00000262238.

PTM databases

iPTMnetiP25490.
PhosphoSitePlusiP25490.

Polymorphism and mutation databases

DMDMi3915889.

Proteomic databases

EPDiP25490.
MaxQBiP25490.
PaxDbiP25490.
PeptideAtlasiP25490.
PRIDEiP25490.

Protocols and materials databases

DNASUi7528.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000262238; ENSP00000262238; ENSG00000100811.
GeneIDi7528.
KEGGihsa:7528.
UCSCiuc001ygy.3. human.

Organism-specific databases

CTDi7528.
DisGeNETi7528.
GeneCardsiYY1.
HGNCiHGNC:12856. YY1.
HPAiCAB009392.
HPA001119.
MIMi600013. gene.
neXtProtiNX_P25490.
OpenTargetsiENSG00000100811.
PharmGKBiPA37445.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1721. Eukaryota.
COG5048. LUCA.
GeneTreeiENSGT00760000118771.
HOGENOMiHOG000008232.
HOVERGENiHBG006823.
InParanoidiP25490.
KOiK09201.
OMAiGGRKWEQ.
OrthoDBiEOG091G03FM.
PhylomeDBiP25490.
TreeFamiTF106493.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000100811-MONOMER.
ReactomeiR-HSA-5617472. Activation of anterior HOX genes in hindbrain development during early embryogenesis.
R-HSA-5689603. UCH proteinases.
R-HSA-5696394. DNA Damage Recognition in GG-NER.
R-HSA-8866910. TFAP2 (AP-2) family regulates transcription of growth factors and their receptors.
SignaLinkiP25490.
SIGNORiP25490.

Miscellaneous databases

ChiTaRSiYY1. human.
EvolutionaryTraceiP25490.
GeneWikiiYY1.
GenomeRNAii7528.
PMAP-CutDBP25490.
PROiP25490.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000100811.
CleanExiHS_YY1.
ExpressionAtlasiP25490. baseline and differential.
GenevisibleiP25490. HS.

Family and domain databases

Gene3Di3.30.160.60. 4 hits.
InterProiIPR017114. TF_Yin_yang.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
PfamiPF00096. zf-C2H2. 1 hit.
[Graphical view]
PIRSFiPIRSF037113. TF_Yin_yang. 1 hit.
SMARTiSM00355. ZnF_C2H2. 4 hits.
[Graphical view]
PROSITEiPS00028. ZINC_FINGER_C2H2_1. 4 hits.
PS50157. ZINC_FINGER_C2H2_2. 4 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiTYY1_HUMAN
AccessioniPrimary (citable) accession number: P25490
Secondary accession number(s): Q14935
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: December 15, 1998
Last modified: November 30, 2016
This is version 194 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, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 14
    Human chromosome 14: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.