CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-005403
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Transcriptional repressor protein YY1 
Protein Synonyms/Alias
 Delta transcription factor; INO80 complex subunit S; NF-E1; Yin and yang 1; YY-1 
Gene Name
 YY1 
Gene Synonyms/Alias
 INO80S 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
183GGKKSGKKSYLSGGAubiquitination[1]
203GGADPGNKKWEQKQVubiquitination[1, 2, 3]
204GADPGNKKWEQKQVQubiquitination[1]
208GNKKWEQKQVQIKTLubiquitination[1]
258YSEYMTGKKLPPGGIubiquitination[2]
274GIDLSDPKQLAEFARubiquitination[1, 2]
288RMKPRKIKEDDAPRTsumoylation[4, 5]
288RMKPRKIKEDDAPRTubiquitination[2]
301RTIACPHKGCTKMFRubiquitination[6]
305CPHKGCTKMFRDNSAubiquitination[1, 6]
332HVCAECGKAFVESSKubiquitination[1, 6, 7]
339KAFVESSKLKRHQLVubiquitination[1, 6]
341FVESSKLKRHQLVHTubiquitination[1]
393PFDGCNKKFAQSTNLubiquitination[1]
401FAQSTNLKSHILTHAubiquitination[1, 8]
Reference
 [1] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [2] Systematic and quantitative assessment of the ubiquitin-modified proteome.
 Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP.
 Mol Cell. 2011 Oct 21;44(2):325-40. [PMID: 21906983]
 [3] Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
 Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA.
 Mol Cell Proteomics. 2012 May;11(5):148-59. [PMID: 22505724]
 [4] PIASy-mediated sumoylation of Yin Yang 1 depends on their interaction but not the RING finger.
 Deng Z, Wan M, Sui G.
 Mol Cell Biol. 2007 May;27(10):3780-92. [PMID: 17353273]
 [5] Targeted identification of SUMOylation sites in human proteins using affinity enrichment and paralog-specific reporter ions.
 Lamoliatte F, Bonneil E, Durette C, Caron-Lizotte O, Wildemann D, Zerweck J, Wenschuh H, Thibault P.
 Mol Cell Proteomics. 2013 Jun 7;. [PMID: 23750026]
 [6] Integrated proteomic analysis of post-translational modifications by serial enrichment.
 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA.
 Nat Methods. 2013 Jul;10(7):634-7. [PMID: 23749302]
 [7] Global identification of modular cullin-RING ligase substrates.
 Emanuele MJ, Elia AE, Xu Q, Thoma CR, Izhar L, Leng Y, Guo A, Chen YN, Rush J, Hsu PW, Yen HC, Elledge SJ.
 Cell. 2011 Oct 14;147(2):459-74. [PMID: 21963094]
 [8] Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass.
 Povlsen LK, Beli P, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker-Jensen S, Mailand N, Choudhary C.
 Nat Cell Biol. 2012 Oct;14(10):1089-98. [PMID: 23000965] 
Functional Description
 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. 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). 
Sequence Annotation
 ZN_FING 296 320 C2H2-type 1.
 ZN_FING 325 347 C2H2-type 2.
 ZN_FING 353 377 C2H2-type 3.
 ZN_FING 383 407 C2H2-type 4.
 REGION 257 341 Involved in nuclear matrix association.
 REGION 333 371 Involved in repression of activated
 REGION 371 397 Involved in masking transactivation
 METAL 298 298 Zinc 1.
 METAL 303 303 Zinc 1.
 METAL 316 316 Zinc 1.
 METAL 320 320 Zinc 1.
 METAL 327 327 Zinc 2.
 METAL 330 330 Zinc 2.
 METAL 343 343 Zinc 2.
 METAL 347 347 Zinc 2.
 METAL 355 355 Zinc 3.
 METAL 360 360 Zinc 3.
 METAL 373 373 Zinc 3.
 METAL 377 377 Zinc 3.
 METAL 385 385 Zinc 4.
 METAL 390 390 Zinc 4.
 METAL 403 403 Zinc 4.
 METAL 407 407 Zinc 4.
 MOD_RES 118 118 Phosphoserine.
 MOD_RES 247 247 Phosphoserine.
 MOD_RES 378 378 Phosphothreonine.  
Keyword
 3D-structure; Activator; ADP-ribosylation; Complete proteome; Differentiation; Direct protein sequencing; DNA damage; DNA recombination; DNA repair; DNA-binding; Metal-binding; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Repeat; Repressor; Spermatogenesis; Transcription; Transcription regulation; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 414 AA 
Protein Sequence
MASGDTLYIA TDGSEMPAEI VELHEIEVET IPVETIETTV VGEEEEEDDD DEDGGGGDHG 60
GGGGHGHAGH HHHHHHHHHH PPMIALQPLV TDDPTQVHHH QEVILVQTRE EVVGGDDSDG 120
LRAEDGFEDQ ILIPVPAPAG GDDDYIEQTL VTVAAAGKSG GGGSSSSGGG RVKKGGGKKS 180
GKKSYLSGGA GAAGGGGADP GNKKWEQKQV QIKTLEGEFS VTMWSSDEKK DIDHETVVEE 240
QIIGENSPPD YSEYMTGKKL PPGGIPGIDL SDPKQLAEFA RMKPRKIKED DAPRTIACPH 300
KGCTKMFRDN SAMRKHLHTH GPRVHVCAEC GKAFVESSKL KRHQLVHTGE KPFQCTFEGC 360
GKRFSLDFNL RTHVRIHTGD RPYVCPFDGC NKKFAQSTNL KSHILTHAKA KNNQ 414 
Gene Ontology
 GO:0031011; C:Ino80 complex; IDA:UniProtKB.
 GO:0016363; C:nuclear matrix; IEA:UniProtKB-SubCell.
 GO:0031519; C:PcG protein complex; IEA:Compara.
 GO:0005886; C:plasma membrane; IDA:HPA.
 GO:0005667; C:transcription factor complex; IEA:Compara.
 GO:0000400; F:four-way junction DNA binding; IDA:UniProtKB.
 GO:0003723; F:RNA binding; IDA:MGI.
 GO:0001078; F:RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription; ISS:BHF-UCL.
 GO:0003713; F:transcription coactivator activity; TAS:ProtInc.
 GO:0003714; F:transcription corepressor activity; TAS:ProtInc.
 GO:0044212; F:transcription regulatory region DNA binding; IDA:MGI.
 GO:0008270; F:zinc ion binding; TAS:ProtInc.
 GO:0009952; P:anterior/posterior pattern specification; IEA:Compara.
 GO:0048593; P:camera-type eye morphogenesis; IEA:Compara.
 GO:0030154; P:cell differentiation; IEA:UniProtKB-KW.
 GO:0034644; P:cellular response to UV; IMP:UniProtKB.
 GO:0051276; P:chromosome organization; IEA:Compara.
 GO:0000724; P:double-strand break repair via homologous recombination; IMP:UniProtKB.
 GO:0034696; P:response to prostaglandin F stimulus; IEA:Compara.
 GO:0010225; P:response to UV-C; IMP:UniProtKB.
 GO:0006403; P:RNA localization; IEA:Compara.
 GO:0007283; P:spermatogenesis; IEA:UniProtKB-KW. 
Interpro
 IPR017114; TF_Yin_yang.
 IPR007087; Znf_C2H2.
 IPR015880; Znf_C2H2-like.
 IPR013087; Znf_C2H2/integrase_DNA-bd. 
Pfam
 PF00096; zf-C2H2 
SMART
 SM00355; ZnF_C2H2 
PROSITE
 PS00028; ZINC_FINGER_C2H2_1
 PS50157; ZINC_FINGER_C2H2_2 
PRINTS