H3Y2_HUMAN
ID H3Y2_HUMAN Reviewed; 147 AA.
AC P0DPK5;
DT 12-SEP-2018, integrated into UniProtKB/Swiss-Prot.
DT 12-SEP-2018, sequence version 1.
DT 03-AUG-2022, entry version 20.
DE RecName: Full=Histone H3.X {ECO:0000303|PubMed:20819935};
DE AltName: Full=Histone H3.Y2 {ECO:0000305};
GN Name=H3Y2 {ECO:0000312|HGNC:HGNC:43734};
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=15372022; DOI=10.1038/nature02919;
RA Schmutz J., Martin J., Terry A., Couronne O., Grimwood J., Lowry S.,
RA Gordon L.A., Scott D., Xie G., Huang W., Hellsten U., Tran-Gyamfi M.,
RA She X., Prabhakar S., Aerts A., Altherr M., Bajorek E., Black S.,
RA Branscomb E., Caoile C., Challacombe J.F., Chan Y.M., Denys M.,
RA Detter J.C., Escobar J., Flowers D., Fotopulos D., Glavina T., Gomez M.,
RA Gonzales E., Goodstein D., Grigoriev I., Groza M., Hammon N., Hawkins T.,
RA Haydu L., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A.,
RA Lopez F., Lou Y., Martinez D., Medina C., Morgan J., Nandkeshwar R.,
RA Noonan J.P., Pitluck S., Pollard M., Predki P., Priest J., Ramirez L.,
RA Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., Thayer N.,
RA Tice H., Tsai M., Ustaszewska A., Vo N., Wheeler J., Wu K., Yang J.,
RA Dickson M., Cheng J.-F., Eichler E.E., Olsen A., Pennacchio L.A.,
RA Rokhsar D.S., Richardson P., Lucas S.M., Myers R.M., Rubin E.M.;
RT "The DNA sequence and comparative analysis of human chromosome 5.";
RL Nature 431:268-274(2004).
RN [2]
RP FUNCTION, SUBCELLULAR LOCATION, SUBUNIT, AND TISSUE SPECIFICITY.
RX PubMed=20819935; DOI=10.1083/jcb.201002043;
RA Wiedemann S.M., Mildner S.N., Boenisch C., Israel L., Maiser A.,
RA Matheisl S., Straub T., Merkl R., Leonhardt H., Kremmer E., Schermelleh L.,
RA Hake S.B.;
RT "Identification and characterization of two novel primate-specific histone
RT H3 variants, H3.X and H3.Y.";
RL J. Cell Biol. 190:777-791(2010).
CC -!- FUNCTION: Primate-specific variant histone H3, which constitutes a core
CC component of nucleosomes (PubMed:20819935). Nucleosomes wrap and
CC compact DNA into chromatin, limiting DNA accessibility to the cellular
CC machineries which require DNA as a template. Histones thereby play a
CC central role in transcription regulation, DNA repair, DNA replication
CC and chromosomal stability. DNA accessibility is regulated via a complex
CC set of post-translational modifications of histones, also called
CC histone code, and nucleosome remodeling (Probable).
CC {ECO:0000269|PubMed:20819935, ECO:0000305}.
CC -!- SUBUNIT: The nucleosome is a histone octamer containing two molecules
CC each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and
CC two H2A-H2B heterodimers (PubMed:20819935). The octamer wraps
CC approximately 147 bp of DNA (Probable). {ECO:0000269|PubMed:20819935,
CC ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:20819935}. Chromosome
CC {ECO:0000305|PubMed:20819935}.
CC -!- TISSUE SPECIFICITY: Expressed at low level in some tissues, such as
CC testis and brain. {ECO:0000269|PubMed:20819935}.
CC -!- PTM: Acetylation is generally linked to gene activation. Acetylation on
CC Lys-10 (H3K9ac) impairs methylation at Arg-9 (H3R8me2s). Acetylation on
CC Lys-19 (H3K18ac) and Lys-24 (H3K24ac) favors methylation at Arg-18
CC (H3R17me). {ECO:0000250|UniProtKB:P84243}.
CC -!- PTM: Citrullination at Arg-9 (H3R8ci) and/or Arg-18 (H3R17ci) impairs
CC methylation and represses transcription.
CC {ECO:0000250|UniProtKB:P84243}.
CC -!- PTM: Asymmetric dimethylation at Arg-18 (H3R17me2a) is linked to gene
CC activation. Symmetric dimethylation at Arg-9 (H3R8me2s) is linked to
CC gene repression. Asymmetric dimethylation at Arg-3 (H3R2me2a) is linked
CC to gene repression and is mutually exclusive with H3 Lys-5 methylation
CC (H3K4me2 and H3K4me3). H3R2me2a is present at the 3' of genes
CC regardless of their transcription state and is enriched on inactive
CC promoters, while it is absent on active promoters.
CC {ECO:0000250|UniProtKB:P84243}.
CC -!- PTM: Methylation at Lys-5 (H3K4me) facilitates subsequent acetylation
CC of H3 and H4. Methylation at Lys-10 (H3K9me) and Lys-28 (H3K27me),
CC which are linked to gene repression, are underrepresented. Methylation
CC at Lys-10 (H3K9me) is a specific target for HP1 proteins (CBX1, CBX3
CC and CBX5) and prevents subsequent acetylation of H3 and H4.
CC {ECO:0000250|UniProtKB:P84243}.
CC -!- PTM: Phosphorylation at Thr-7 (H3T6ph) is a specific tag for epigenetic
CC transcriptional activation that prevents demethylation of Lys-5
CC (H3K4me) by LSD1/KDM1A. At centromeres, specifically phosphorylated at
CC Thr-12 (H3T11ph) from prophase to early anaphase. Phosphorylation at
CC Thr-12 (H3T11ph) is a specific tag for epigenetic transcriptional
CC activation that promotes demethylation of Lys-10 (H3K9me).
CC Phosphorylation at Tyr-42 (H3Y41ph) promotes exclusion of CBX5 (HP1
CC alpha) from chromatin. {ECO:0000250|UniProtKB:P84243}.
CC -!- PTM: Lysine deamination at Lys-5 (H3K4all) to form allysine. Allysine
CC formation only takes place on H3K4me3 and results in gene repression.
CC {ECO:0000250|UniProtKB:P84243}.
CC -!- PTM: Crotonylation (Kcr) is specifically present in male germ cells and
CC marks testis-specific genes in post-meiotic cells, including X-linked
CC genes that escape sex chromosome inactivation in haploid cells.
CC Crotonylation marks active promoters and enhancers and confers
CC resistance to transcriptional repressors. It is also associated with
CC post-meiotically activated genes on autosomes.
CC {ECO:0000250|UniProtKB:P84243}.
CC -!- PTM: Butyrylation of histones marks active promoters and competes with
CC histone acetylation. It is present during late spermatogenesis.
CC {ECO:0000250|UniProtKB:P68433}.
CC -!- SIMILARITY: Belongs to the histone H3 family. {ECO:0000305}.
CC -!- CAUTION: Could be the product of a pseudogene. {ECO:0000305}.
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DR EMBL; AC233724; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR AlphaFoldDB; P0DPK5; -.
DR SMR; P0DPK5; -.
DR MassIVE; P0DPK5; -.
DR PeptideAtlas; P0DPK5; -.
DR Ensembl; ENST00000600799.3; ENSP00000497053.1; ENSG00000268799.4.
DR MANE-Select; ENST00000600799.3; ENSP00000497053.1; NM_001371919.1; NP_001358848.1.
DR GeneCards; H3Y2; -.
DR HGNC; HGNC:43734; H3Y2.
DR HPA; ENSG00000268799; Not detected.
DR neXtProt; NX_P0DPK5; -.
DR OpenTargets; ENSG00000268799; -.
DR VEuPathDB; HostDB:ENSG00000268799; -.
DR GeneTree; ENSGT01050000244889; -.
DR OMA; ARKATDW; -.
DR SIGNOR; P0DPK5; -.
DR Pharos; P0DPK5; Tdark.
DR Proteomes; UP000005640; Chromosome 5.
DR Bgee; ENSG00000268799; Expressed in blood and 4 other tissues.
DR GO; GO:0000786; C:nucleosome; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0046982; F:protein heterodimerization activity; IEA:InterPro.
DR GO; GO:0030527; F:structural constituent of chromatin; IEA:InterPro.
DR Gene3D; 1.10.20.10; -; 1.
DR InterPro; IPR009072; Histone-fold.
DR InterPro; IPR007125; Histone_H2A/H2B/H3.
DR InterPro; IPR000164; Histone_H3/CENP-A.
DR PANTHER; PTHR11426; PTHR11426; 1.
DR Pfam; PF00125; Histone; 1.
DR PRINTS; PR00622; HISTONEH3.
DR SMART; SM00428; H3; 1.
DR SUPFAM; SSF47113; SSF47113; 1.
DR PROSITE; PS00959; HISTONE_H3_2; 1.
PE 5: Uncertain;
KW Acetylation; Chromosome; Citrullination; Hydroxylation; Methylation;
KW Nucleus; Phosphoprotein; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT CHAIN 2..147
FT /note="Histone H3.X"
FT /id="PRO_0000445073"
FT REGION 1..43
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 3
FT /note="Asymmetric dimethylarginine"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 3
FT /note="Citrulline; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 4
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 5
FT /note="Allysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 5
FT /note="N6,N6,N6-trimethyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 5
FT /note="N6,N6-dimethyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 5
FT /note="N6-(2-hydroxyisobutyryl)lysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 5
FT /note="N6-(beta-hydroxybutyryl)lysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 5
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 5
FT /note="N6-crotonyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 5
FT /note="N6-methyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 6
FT /note="5-glutamyl dopamine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P68431"
FT MOD_RES 6
FT /note="5-glutamyl serotonin; alternate"
FT /evidence="ECO:0000250|UniProtKB:P68431"
FT MOD_RES 7
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 9
FT /note="Citrulline; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 9
FT /note="Symmetric dimethylarginine"
FT /evidence="ECO:0000250|UniProtKB:P84244"
FT MOD_RES 10
FT /note="N6,N6,N6-trimethyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 10
FT /note="N6,N6-dimethyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 10
FT /note="N6-(2-hydroxyisobutyryl)lysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 10
FT /note="N6-(beta-hydroxybutyryl)lysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 10
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 10
FT /note="N6-butyryllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 10
FT /note="N6-crotonyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 10
FT /note="N6-lactoyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P68431"
FT MOD_RES 10
FT /note="N6-methyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 12
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 18
FT /note="Asymmetric dimethylarginine"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 18
FT /note="Citrulline; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 19
FT /note="N6-(2-hydroxyisobutyryl)lysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 19
FT /note="N6-(beta-hydroxybutyryl)lysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 19
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 19
FT /note="N6-butyryllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 19
FT /note="N6-crotonyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 19
FT /note="N6-glutaryllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 19
FT /note="N6-lactoyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P68431"
FT MOD_RES 19
FT /note="N6-methyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 24
FT /note="N6-(2-hydroxyisobutyryl)lysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 24
FT /note="N6-(beta-hydroxybutyryl)lysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 24
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 24
FT /note="N6-butyryllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 24
FT /note="N6-crotonyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 24
FT /note="N6-glutaryllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 24
FT /note="N6-lactoyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P68431"
FT MOD_RES 24
FT /note="N6-methyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 27
FT /note="Citrulline"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 28
FT /note="N6,N6,N6-trimethyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 28
FT /note="N6,N6-dimethyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 28
FT /note="N6-(2-hydroxyisobutyryl)lysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 28
FT /note="N6-(beta-hydroxybutyryl)lysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 28
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 28
FT /note="N6-crotonyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 28
FT /note="N6-glutaryllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 28
FT /note="N6-lactoyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P68431"
FT MOD_RES 28
FT /note="N6-methyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 37
FT /note="N6,N6,N6-trimethyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 37
FT /note="N6,N6-dimethyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 37
FT /note="N6-(2-hydroxyisobutyryl)lysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 37
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 37
FT /note="N6-methyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 38
FT /note="N6-methyllysine"
FT /evidence="ECO:0000250|UniProtKB:P68431"
FT MOD_RES 42
FT /note="Phosphotyrosine"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 57
FT /note="N6,N6,N6-trimethyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 57
FT /note="N6-(2-hydroxyisobutyryl)lysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 57
FT /note="N6-(beta-hydroxybutyryl)lysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 57
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 57
FT /note="N6-crotonyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 57
FT /note="N6-glutaryllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 57
FT /note="N6-lactoyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P68433"
FT MOD_RES 57
FT /note="N6-methyllysine"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 57
FT /note="N6-succinyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 58
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 65
FT /note="N6-(2-hydroxyisobutyryl)lysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 65
FT /note="N6-methyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 87
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P84243"
FT MOD_RES 108
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:Q71DI3"
SQ SEQUENCE 147 AA; 16466 MW; 376ED0387510DDDF CRC64;
MARTKQTARK ATAWQAPRKP LATKAARKRA SPTGGIKKPH RYKPGTLALR EIRKYQKSTQ
LLLRKLPFQR LVREIAQAIS PDLRFQSAAI GALQEASEAY LVQLFEDTNL CAIHARRVTI
MPRDMQLARR LRGEGAGEPT LLGNLAL
