H2B4_ARATH
ID H2B4_ARATH Reviewed; 138 AA.
AC Q9ZUS0;
DT 30-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 136.
DE RecName: Full=Histone H2B.4;
DE AltName: Full=HTB5;
GN OrderedLocusNames=At2g37470; ORFNames=F3G5.26;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP UBIQUITINATION AT LYS-135, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=17554311; DOI=10.1038/nature05864;
RA Sridhar V.V., Kapoor A., Zhang K., Zhu J., Zhou T., Hasegawa P.M.,
RA Bressan R.A., Zhu J.-K.;
RT "Control of DNA methylation and heterochromatic silencing by histone H2B
RT deubiquitination.";
RL Nature 447:735-738(2007).
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 {ECO:0000250}. Chromosome {ECO:0000250}.
CC -!- PTM: Can be acetylated to form H2BK6ac, H2BK33ac and H2BK34ac.
CC {ECO:0000250}.
CC -!- PTM: Monoubiquitinated by BRE1 to form H2BK143ub1 and deubiquitinated
CC by UBP26. Required for heterochromatic histone H3 di- and
CC trimethylation at H3K4me. May give a specific tag for epigenetic
CC transcriptional activation.
CC -!- SIMILARITY: Belongs to the histone H2B family. {ECO:0000305}.
CC -!- CAUTION: To ensure consistency between histone entries, we follow the
CC 'Brno' nomenclature for histone modifications, with positions referring
CC to those used in the literature for the 'closest' model organism. Due
CC to slight variations in histone sequences between organisms and to the
CC presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the
CC actual positions of modified amino acids in the sequence generally
CC differ. In this entry the following conventions are used: H2BK6ac =
CC acetylated Lys-8; H2BK33ac = acetylated Lys-29; H2BK34ac = acetylated
CC Lys-30; H2BK143ub1 = monoubiquitinated Lys-135. {ECO:0000305}.
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DR EMBL; AC005896; AAC98063.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC09404.1; -; Genomic_DNA.
DR EMBL; BT005206; AAO63270.1; -; mRNA.
DR EMBL; AY087125; AAM64683.1; -; mRNA.
DR PIR; B84793; B84793.
DR RefSeq; NP_181283.1; NM_129302.3.
DR AlphaFoldDB; Q9ZUS0; -.
DR SMR; Q9ZUS0; -.
DR STRING; 3702.AT2G37470.1; -.
DR iPTMnet; Q9ZUS0; -.
DR PaxDb; Q9ZUS0; -.
DR PRIDE; Q9ZUS0; -.
DR ProteomicsDB; 222371; -.
DR EnsemblPlants; AT2G37470.1; AT2G37470.1; AT2G37470.
DR GeneID; 818324; -.
DR Gramene; AT2G37470.1; AT2G37470.1; AT2G37470.
DR KEGG; ath:AT2G37470; -.
DR Araport; AT2G37470; -.
DR TAIR; locus:2049857; AT2G37470.
DR eggNOG; KOG1744; Eukaryota.
DR HOGENOM; CLU_075666_1_3_1; -.
DR InParanoid; Q9ZUS0; -.
DR OMA; SKEMSIM; -.
DR OrthoDB; 1536672at2759; -.
DR PhylomeDB; Q9ZUS0; -.
DR PRO; PR:Q9ZUS0; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q9ZUS0; baseline and differential.
DR Genevisible; Q9ZUS0; AT.
DR GO; GO:0005783; C:endoplasmic reticulum; HDA:TAIR.
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 1: Evidence at protein level;
KW Acetylation; Chromosome; DNA-binding; Isopeptide bond; Methylation;
KW Nucleosome core; Nucleus; Reference proteome; Ubl conjugation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250|UniProtKB:Q9LQQ4"
FT CHAIN 2..138
FT /note="Histone H2B.4"
FT /id="PRO_0000238691"
FT REGION 1..48
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 2
FT /note="N,N,N-trimethylalanine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9LQQ4"
FT MOD_RES 2
FT /note="N,N-dimethylalanine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9LQQ4"
FT MOD_RES 2
FT /note="N-methylalanine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9LQQ4"
FT MOD_RES 4
FT /note="N6-methyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q9LZT0"
FT MOD_RES 8
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q9LQQ4"
FT MOD_RES 13
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:O23629"
FT MOD_RES 14
FT /note="N6,N6-dimethyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q9FFC0"
FT MOD_RES 18
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:O23629"
FT MOD_RES 23
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:O23629"
FT MOD_RES 29
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q9LQQ4"
FT MOD_RES 30
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q9LQQ4"
FT CROSSLNK 135
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000250|UniProtKB:Q9LQQ4"
SQ SEQUENCE 138 AA; 15082 MW; 5E7206140B3B5863 CRC64;
MAPKAAEKKP AEKKPAGKAP AEKLPKAEKK ISKDAGGSEK KKKKSKKSVE TYKIYIFKVL
KQVHPDVGIS GKAMGIMNSF INDIFEKLAQ ESSKLARYNK KPTITSREIQ TAVRLVLPGE
LAKHAVSEGT KAVTKFTS
