ID YNG2_YEAST Reviewed; 282 AA.
AC P38806; D3DL42;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 27-MAR-2024, entry version 188.
DE RecName: Full=Chromatin modification-related protein YNG2;
DE AltName: Full=ESA1-associated factor 4;
DE AltName: Full=ING1 homolog 2;
GN Name=YNG2; Synonyms=EAF4, NBN1; OrderedLocusNames=YHR090C;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8091229; DOI=10.1126/science.8091229;
RA Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J., Du Z.,
RA Favello A., Fulton L., Gattung S., Geisel C., Kirsten J., Kucaba T.,
RA Hillier L.W., Jier M., Johnston L., Langston Y., Latreille P., Louis E.J.,
RA Macri C., Mardis E., Menezes S., Mouser L., Nhan M., Rifkin L., Riles L.,
RA St Peter H., Trevaskis E., Vaughan K., Vignati D., Wilcox L., Wohldman P.,
RA Waterston R., Wilson R., Vaudin M.;
RT "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome
RT VIII.";
RL Science 265:2077-2082(1994).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [3]
RP FUNCTION, SUBCELLULAR LOCATION, AND IDENTIFICATION IN THE NUA4 COMPLEX.
RX PubMed=10805724; DOI=10.1128/mcb.20.11.3807-3816.2000;
RA Loewith R., Meijer M., Lees-Miller S.P., Riabowol K., Young D.;
RT "Three yeast proteins related to the human candidate tumor suppressor
RT p33(ING1) are associated with histone acetyltransferase activities.";
RL Mol. Cell. Biol. 20:3807-3816(2000).
RN [4]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=11544250; DOI=10.1074/jbc.m102531200;
RA Choy J.S., Tobe B.T.D., Huh J.H., Kron S.J.;
RT "Yng2p-dependent NuA4 histone H4 acetylation activity is required for
RT mitotic and meiotic progression.";
RL J. Biol. Chem. 276:43653-43662(2001).
RN [5]
RP PROTEIN SEQUENCE OF 1-34; 62-70; 107-161; 171-180 AND 184-193,
RP IDENTIFICATION IN THE NUA4 COMPLEX, AND FUNCTION.
RX PubMed=11604499; DOI=10.1128/mcb.21.22.7629-7640.2001;
RA Nourani A., Doyon Y., Utley R.T., Allard S., Lane W.S., Cote J.;
RT "Role of an ING1 growth regulator in transcriptional activation and
RT targeted histone acetylation by the NuA4 complex.";
RL Mol. Cell. Biol. 21:7629-7640(2001).
RN [6]
RP FUNCTION.
RX PubMed=12417725; DOI=10.1128/mcb.22.23.8215-8225.2002;
RA Choy J.S., Kron S.J.;
RT "NuA4 subunit Yng2 function in intra-S-phase DNA damage response.";
RL Mol. Cell. Biol. 22:8215-8225(2002).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=14690591; DOI=10.1016/s1097-2765(03)00476-3;
RA Hazbun T.R., Malmstroem L., Anderson S., Graczyk B.J., Fox B., Riffle M.,
RA Sundin B.A., Aranda J.D., McDonald W.H., Chiu C.-H., Snydsman B.E.,
RA Bradley P., Muller E.G.D., Fields S., Baker D., Yates J.R. III, Davis T.N.;
RT "Assigning function to yeast proteins by integration of technologies.";
RL Mol. Cell 12:1353-1365(2003).
RN [8]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [9]
RP IDENTIFICATION IN THE NUA4 COMPLEX, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RX PubMed=15485911; DOI=10.1128/mcb.24.21.9424-9436.2004;
RA Zhang H., Richardson D.O., Roberts D.N., Utley R.T., Erdjument-Bromage H.,
RA Tempst P., Cote J., Cairns B.R.;
RT "The Yaf9 component of the SWR1 and NuA4 complexes is required for proper
RT gene expression, histone H4 acetylation, and Htz1 replacement near
RT telomeres.";
RL Mol. Cell. Biol. 24:9424-9436(2004).
RN [10]
RP IDENTIFICATION IN THE NUA4 COMPLEX, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RX PubMed=15045029; DOI=10.1371/journal.pbio.0020131;
RA Kobor M.S., Venkatasubrahmanyam S., Meneghini M.D., Gin J.W.,
RA Jennings J.L., Link A.J., Madhani H.D., Rine J.;
RT "A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p
RT deposits histone variant H2A.Z into euchromatin.";
RL PLoS Biol. 2:587-599(2004).
RN [11]
RP IDENTIFICATION IN THE NUA4 COMPLEX, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RX PubMed=15353583; DOI=10.1073/pnas.0405753101;
RA Krogan N.J., Baetz K., Keogh M.-C., Datta N., Sawa C., Kwok T.C.Y.,
RA Thompson N.J., Davey M.G., Pootoolal J., Hughes T.R., Emili A.,
RA Buratowski S., Hieter P., Greenblatt J.F.;
RT "Regulation of chromosome stability by the histone H2A variant Htz1, the
RT Swr1 chromatin remodeling complex, and the histone acetyltransferase
RT NuA4.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:13513-13518(2004).
RN [12]
RP DOMAIN PHD-TYPE ZINC-FINGER, AND INTERACTION WITH HISTONES H3K4ME3 AND
RP H3K4ME2.
RX PubMed=16728974; DOI=10.1038/nature04835;
RA Shi X., Hong T., Walter K.L., Ewalt M., Michishita E., Hung T., Carney D.,
RA Pena P., Lan F., Kaadige M.R., Lacoste N., Cayrou C., Davrazou F., Saha A.,
RA Cairns B.R., Ayer D.E., Kutateladze T.G., Shi Y., Cote J., Chua K.F.,
RA Gozani O.;
RT "ING2 PHD domain links histone H3 lysine 4 methylation to active gene
RT repression.";
RL Nature 442:96-99(2006).
RN [13]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [14]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-183; THR-185 AND SER-188, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
CC -!- FUNCTION: Component of the NuA4 histone acetyltransferase complex which
CC is involved in transcriptional activation of selected genes principally
CC by acetylation of nucleosomal histone H4 and H2A. The NuA4 complex is
CC also involved in DNA repair. Involved in cell cycle progression and
CC meiosis. {ECO:0000269|PubMed:10805724, ECO:0000269|PubMed:11544250,
CC ECO:0000269|PubMed:11604499, ECO:0000269|PubMed:12417725}.
CC -!- SUBUNIT: Interacts with H3K4me3 and to a lesser extent with H3K4me2.
CC Component of the NuA4 histone acetyltransferase complex composed of at
CC least ACT1, ARP4, YAF9, VID21, SWC4, EAF3, EAF5, EAF6, EAF7, EPL1,
CC ESA1, TRA1 and YNG2. {ECO:0000269|PubMed:10805724,
CC ECO:0000269|PubMed:11604499, ECO:0000269|PubMed:15045029,
CC ECO:0000269|PubMed:15353583, ECO:0000269|PubMed:15485911,
CC ECO:0000269|PubMed:16728974}.
CC -!- INTERACTION:
CC P38806; P43572: EPL1; NbExp=10; IntAct=EBI-24622, EBI-22792;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:10805724,
CC ECO:0000269|PubMed:11544250, ECO:0000269|PubMed:14562095}.
CC -!- DOMAIN: The PHD-type zinc finger mediates the binding to H3K4me3.
CC {ECO:0000269|PubMed:16728974}.
CC -!- SIMILARITY: Belongs to the ING family. {ECO:0000305}.
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DR EMBL; U00060; AAB68930.1; -; Genomic_DNA.
DR EMBL; BK006934; DAA06786.1; -; Genomic_DNA.
DR PIR; S46722; S46722.
DR RefSeq; NP_011958.1; NM_001179220.1.
DR PDB; 2MUM; NMR; -; A=222-271.
DR PDB; 5J9Q; X-ray; 3.25 A; D/H/K=1-120.
DR PDB; 5J9T; X-ray; 2.70 A; D/H/L=1-120.
DR PDB; 5J9U; X-ray; 2.95 A; D/H/K=1-120.
DR PDB; 5J9W; X-ray; 2.80 A; D/H/L=1-120.
DR PDB; 7VVU; EM; 3.40 A; V=1-282.
DR PDB; 7VVZ; EM; 8.80 A; V=1-282.
DR PDBsum; 2MUM; -.
DR PDBsum; 5J9Q; -.
DR PDBsum; 5J9T; -.
DR PDBsum; 5J9U; -.
DR PDBsum; 5J9W; -.
DR PDBsum; 7VVU; -.
DR PDBsum; 7VVZ; -.
DR AlphaFoldDB; P38806; -.
DR BMRB; P38806; -.
DR EMDB; EMD-32148; -.
DR EMDB; EMD-32150; -.
DR SMR; P38806; -.
DR BioGRID; 36525; 600.
DR ComplexPortal; CPX-3155; NuA4 histone acetyltransferase complex.
DR ComplexPortal; CPX-3185; Piccolo NuA4 histone acetyltransferase complex.
DR DIP; DIP-2095N; -.
DR IntAct; P38806; 19.
DR MINT; P38806; -.
DR STRING; 4932.YHR090C; -.
DR iPTMnet; P38806; -.
DR MaxQB; P38806; -.
DR PaxDb; 4932-YHR090C; -.
DR PeptideAtlas; P38806; -.
DR EnsemblFungi; YHR090C_mRNA; YHR090C; YHR090C.
DR GeneID; 856490; -.
DR KEGG; sce:YHR090C; -.
DR AGR; SGD:S000001132; -.
DR SGD; S000001132; YNG2.
DR VEuPathDB; FungiDB:YHR090C; -.
DR eggNOG; KOG1973; Eukaryota.
DR GeneTree; ENSGT00940000156619; -.
DR HOGENOM; CLU_031900_2_0_1; -.
DR InParanoid; P38806; -.
DR OMA; GPNCKYE; -.
DR OrthoDB; 3140066at2759; -.
DR BioCyc; YEAST:G3O-31137-MONOMER; -.
DR Reactome; R-SCE-3899300; SUMOylation of transcription cofactors.
DR Reactome; R-SCE-6811555; PI5P Regulates TP53 Acetylation.
DR BioGRID-ORCS; 856490; 6 hits in 10 CRISPR screens.
DR PRO; PR:P38806; -.
DR Proteomes; UP000002311; Chromosome VIII.
DR RNAct; P38806; Protein.
DR GO; GO:0005829; C:cytosol; IDA:SGD.
DR GO; GO:0035267; C:NuA4 histone acetyltransferase complex; IDA:SGD.
DR GO; GO:0000786; C:nucleosome; IDA:ComplexPortal.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0032777; C:piccolo histone acetyltransferase complex; IDA:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0035064; F:methylated histone binding; IDA:UniProtKB.
DR GO; GO:0006338; P:chromatin remodeling; IEA:GOC.
DR GO; GO:0006281; P:DNA repair; IDA:SGD.
DR GO; GO:0006351; P:DNA-templated transcription; NAS:ComplexPortal.
DR GO; GO:0051321; P:meiotic cell cycle; IEA:UniProtKB-KW.
DR GO; GO:0006355; P:regulation of DNA-templated transcription; IBA:GO_Central.
DR CDD; cd16858; ING_ING3_Yng2p; 1.
DR CDD; cd15505; PHD_ING; 1.
DR Gene3D; 6.10.140.1740; -; 1.
DR Gene3D; 3.30.40.10; Zinc/RING finger domain, C3HC4 (zinc finger); 1.
DR InterPro; IPR028651; ING_fam.
DR InterPro; IPR024610; ING_N_histone-binding.
DR InterPro; IPR019786; Zinc_finger_PHD-type_CS.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR019787; Znf_PHD-finger.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR PANTHER; PTHR10333:SF100; CHROMATIN MODIFICATION-RELATED PROTEIN YNG2; 1.
DR PANTHER; PTHR10333; INHIBITOR OF GROWTH PROTEIN; 1.
DR Pfam; PF12998; ING; 1.
DR Pfam; PF00628; PHD; 1.
DR SMART; SM01408; ING; 1.
DR SMART; SM00249; PHD; 1.
DR SUPFAM; SSF57903; FYVE/PHD zinc finger; 1.
DR PROSITE; PS01359; ZF_PHD_1; 1.
DR PROSITE; PS50016; ZF_PHD_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell cycle; Chromatin regulator; Coiled coil;
KW Direct protein sequencing; DNA damage; DNA repair; Meiosis; Metal-binding;
KW Nucleus; Phosphoprotein; Reference proteome; Zinc; Zinc-finger.
FT CHAIN 1..282
FT /note="Chromatin modification-related protein YNG2"
FT /id="PRO_0000212679"
FT ZN_FING 222..271
FT /note="PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 123..217
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 35..86
FT /evidence="ECO:0000255"
FT COMPBIAS 133..162
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 225
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9UK53"
FT BINDING 227
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9UK53"
FT BINDING 238
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9UK53"
FT BINDING 243
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9UK53"
FT BINDING 249
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9UK53"
FT BINDING 252
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9UK53"
FT BINDING 265
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9UK53"
FT BINDING 268
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9UK53"
FT SITE 224
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250|UniProtKB:Q9UK53"
FT SITE 235
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250|UniProtKB:Q9UK53"
FT SITE 239
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250|UniProtKB:Q9UK53"
FT SITE 247
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250|UniProtKB:Q9UK53"
FT MOD_RES 183
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 185
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 188
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT HELIX 3..13
FT /evidence="ECO:0007829|PDB:5J9T"
FT TURN 14..16
FT /evidence="ECO:0007829|PDB:5J9T"
FT HELIX 17..56
FT /evidence="ECO:0007829|PDB:5J9T"
FT STRAND 58..60
FT /evidence="ECO:0007829|PDB:5J9T"
FT HELIX 65..113
FT /evidence="ECO:0007829|PDB:5J9T"
FT STRAND 225..227
FT /evidence="ECO:0007829|PDB:2MUM"
FT TURN 250..254
FT /evidence="ECO:0007829|PDB:2MUM"
FT HELIX 266..270
FT /evidence="ECO:0007829|PDB:2MUM"
SQ SEQUENCE 282 AA; 32086 MW; 110E0A2536547D03 CRC64;
MDPSLVLEQT IQDVSNLPSE FRYLLEEIGS NDLKLIEEKK KYEQKESQIH KFIRQQGSIP
KHPQEDGLDK EIKESLLKCQ SLQREKCVLA NTALFLIARH LNKLEKNIAL LEEDGVLAPV
EEDGDMDSAA EASRESSVVS NSSVKKRRAA SSSGSVPPTL KKKKTSRTSK LQNEIDVSSR
EKSVTPVSPS IEKKIARTKE FKNSRNGKGQ NGSPENEEED KTLYCFCQRV SFGEMVACDG
PNCKYEWFHY DCVNLKEPPK GTWYCPECKI EMEKNKLKRK RN
//
