H2B3_DANRE
ID H2B3_DANRE Reviewed; 126 AA.
AC Q6PC60;
DT 11-JUL-2006, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 132.
DE RecName: Full=Histone H2B 3;
GN Name=hist2h2l; ORFNames=zgc:73093;
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen;
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Eye;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (OCT-2003) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Core component of nucleosome. Nucleosomes wrap and compact
CC 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.
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. The octamer wraps approximately 147 bp of
CC DNA.
CC -!- SUBCELLULAR LOCATION: Nucleus. Chromosome.
CC -!- PTM: Monoubiquitination of Lys-121 by the BRE1 gives a specific tag for
CC epigenetic transcriptional activation and is also prerequisite for
CC histone H3 'Lys-4' and 'Lys-79' methylation.
CC {ECO:0000250|UniProtKB:P33778}.
CC -!- PTM: Phosphorylated on Ser-15 during apoptosis; which facilitates
CC apoptotic chromatin condensation. {ECO:0000250|UniProtKB:P06900}.
CC -!- PTM: GlcNAcylation at Ser-113 promotes monoubiquitination of Lys-121.
CC It fluctuates in response to extracellular glucose, and associates with
CC transcribed genes (By similarity). {ECO:0000250|UniProtKB:P62807}.
CC -!- SIMILARITY: Belongs to the histone H2B family. {ECO:0000305}.
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DR EMBL; BX120005; CAK03634.1; -; Genomic_DNA.
DR EMBL; BC059463; AAH59463.1; -; mRNA.
DR RefSeq; NP_956411.1; NM_200117.1.
DR AlphaFoldDB; Q6PC60; -.
DR SMR; Q6PC60; -.
DR STRING; 7955.ENSDARP00000055912; -.
DR PaxDb; Q6PC60; -.
DR Ensembl; ENSDART00000055913; ENSDARP00000055912; ENSDARG00000068996.
DR Ensembl; ENSDART00000186233; ENSDARP00000156959; ENSDARG00000112150.
DR GeneID; 386920; -.
DR KEGG; dre:386920; -.
DR CTD; 386920; -.
DR ZFIN; ZDB-GENE-031118-36; hist2h2l.
DR eggNOG; KOG1744; Eukaryota.
DR GeneTree; ENSGT01050000244921; -.
DR HOGENOM; CLU_075666_2_1_1; -.
DR InParanoid; Q6PC60; -.
DR OMA; HHEMGIS; -.
DR OrthoDB; 1536672at2759; -.
DR PhylomeDB; Q6PC60; -.
DR TreeFam; TF300212; -.
DR Reactome; R-DRE-110330; Recognition and association of DNA glycosylase with site containing an affected purine.
DR Reactome; R-DRE-110331; Cleavage of the damaged purine.
DR Reactome; R-DRE-171306; Packaging Of Telomere Ends.
DR Reactome; R-DRE-201722; Formation of the beta-catenin:TCF transactivating complex.
DR Reactome; R-DRE-212300; PRC2 methylates histones and DNA.
DR Reactome; R-DRE-2299718; Condensation of Prophase Chromosomes.
DR Reactome; R-DRE-2559580; Oxidative Stress Induced Senescence.
DR Reactome; R-DRE-2559582; Senescence-Associated Secretory Phenotype (SASP).
DR Reactome; R-DRE-2559586; DNA Damage/Telomere Stress Induced Senescence.
DR Reactome; R-DRE-3214815; HDACs deacetylate histones.
DR Reactome; R-DRE-3214847; HATs acetylate histones.
DR Reactome; R-DRE-427359; SIRT1 negatively regulates rRNA expression.
DR Reactome; R-DRE-5250924; B-WICH complex positively regulates rRNA expression.
DR Reactome; R-DRE-5578749; Transcriptional regulation by small RNAs.
DR Reactome; R-DRE-5625886; Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3.
DR Reactome; R-DRE-5689880; Ub-specific processing proteases.
DR Reactome; R-DRE-5693565; Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
DR Reactome; R-DRE-5693571; Nonhomologous End-Joining (NHEJ).
DR Reactome; R-DRE-5693607; Processing of DNA double-strand break ends.
DR Reactome; R-DRE-606279; Deposition of new CENPA-containing nucleosomes at the centromere.
DR Reactome; R-DRE-68616; Assembly of the ORC complex at the origin of replication.
DR Reactome; R-DRE-69473; G2/M DNA damage checkpoint.
DR Reactome; R-DRE-73728; RNA Polymerase I Promoter Opening.
DR Reactome; R-DRE-73772; RNA Polymerase I Promoter Escape.
DR Reactome; R-DRE-8866654; E3 ubiquitin ligases ubiquitinate target proteins.
DR Reactome; R-DRE-8936459; RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function.
DR Reactome; R-DRE-9018519; Estrogen-dependent gene expression.
DR Reactome; R-DRE-9670095; Inhibition of DNA recombination at telomere.
DR PRO; PR:Q6PC60; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 10.
DR Bgee; ENSDARG00000068996; Expressed in brain and 27 other tissues.
DR GO; GO:0000785; C:chromatin; IDA:ZFIN.
DR GO; GO:0000786; C:nucleosome; IEA:UniProtKB-KW.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IBA:GO_Central.
DR GO; GO:0046982; F:protein heterodimerization activity; IEA:InterPro.
DR GO; GO:0030527; F:structural constituent of chromatin; IEA:InterPro.
DR GO; GO:0006334; P:nucleosome assembly; IBA:GO_Central.
DR Gene3D; 1.10.20.10; -; 1.
DR InterPro; IPR009072; Histone-fold.
DR InterPro; IPR007125; Histone_H2A/H2B/H3.
DR InterPro; IPR000558; Histone_H2B.
DR PANTHER; PTHR23428; PTHR23428; 1.
DR Pfam; PF00125; Histone; 1.
DR PRINTS; PR00621; HISTONEH2B.
DR SMART; SM00427; H2B; 1.
DR SUPFAM; SSF47113; SSF47113; 1.
DR PROSITE; PS00357; HISTONE_H2B; 1.
PE 2: Evidence at transcript level;
KW Acetylation; Chromosome; DNA-binding; Glycoprotein; Isopeptide bond;
KW Nucleosome core; Nucleus; Phosphoprotein; Reference proteome;
KW Ubl conjugation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250"
FT CHAIN 2..126
FT /note="Histone H2B 3"
FT /id="PRO_0000244868"
FT REGION 1..34
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 17..32
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 6
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P0C1H4"
FT MOD_RES 13
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P0C1H4"
FT MOD_RES 15
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P06900"
FT MOD_RES 16
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P0C1H4"
FT MOD_RES 21
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P0C1H4"
FT CARBOHYD 113
FT /note="O-linked (GlcNAc) serine"
FT /evidence="ECO:0000250|UniProtKB:P62807"
FT CROSSLNK 121
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000250|UniProtKB:P0C1H4"
SQ SEQUENCE 126 AA; 13948 MW; 17FF749927C2070C CRC64;
MPEPAKSAPA PKKGSKKAVT KTQKKGDKKR RKTRKESYAI YVYKVLKQVH PDTGISSKAM
GIMNSFVNDI FERIAGEASR LAHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT
KYTSSK
