H2B6_ARATH
ID H2B6_ARATH Reviewed; 150 AA.
AC O23629;
DT 30-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 146.
DE RecName: Full=Histone H2B.6;
DE AltName: Full=H2BAt;
DE AltName: Full=HTB9;
GN Name=H2B; OrderedLocusNames=At3g45980; ORFNames=F16L2.190;
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 [MRNA], AND DEVELOPMENTAL STAGE.
RX PubMed=9414552; DOI=10.1104/pp.115.4.1385;
RA Callard D., Mazzolini L.;
RT "Identification of proliferation-induced genes in Arabidopsis thaliana.
RT Characterization of a new member of the highly evolutionarily conserved
RT histone H2A.F/Z variant subfamily.";
RL Plant Physiol. 115:1385-1395(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [3]
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 [4]
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 [5]
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 [6]
RP UBIQUITINATION AT LYS-146, 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).
RN [7]
RP ACETYLATION AT LYS-7; LYS-12; LYS-28; LYS-33; LYS-39 AND LYS-40,
RP METHYLATION AT ALA-2, UBIQUITINATION AT LYS-146, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RX PubMed=17691833; DOI=10.1021/pr0702159;
RA Bergmueller E., Gehrig P.M., Gruissem W.;
RT "Characterization of post-translational modifications of histone H2B-
RT variants isolated from Arabidopsis thaliana.";
RL J. Proteome Res. 6:3655-3668(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 -!- DEVELOPMENTAL STAGE: Strong up-regulation during the S-phase.
CC {ECO:0000269|PubMed:9414552}.
CC -!- PTM: Can be acetylated to form H2BK6ac, H2BK11ac, H2BK22ac, H2BK27ac
CC H2BK33ac and H2BK34ac. {ECO:0000269|PubMed:17691833}.
CC -!- PTM: Mono-, di- or trimethylated at the N-terminus to form
CC H2BA1me1/2/3. H2BA1me2 may be acetylated to form H2BA1me2K6ac and
CC H2BA1me2K6acK11ac. {ECO:0000269|PubMed:17691833}.
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: H2BA1me1/2/3
CC = mono-, di- and trimethylated Ala-2; H2BK6ac = acetylated Lys-7;
CC H2BK11ac = acetylated Lys-12; H2BK22ac = acetylated Lys-28; H2BK27ac =
CC acetylated Lys-33; H2BK33ac = acetylated Lys-39; H2BK34ac = acetylated
CC Lys-40; H2BK143ub1 = monoubiquitinated Lys-146. {ECO:0000305}.
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DR EMBL; Y12576; CAA73156.1; -; mRNA.
DR EMBL; AL162459; CAB82822.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE78097.1; -; Genomic_DNA.
DR EMBL; BT006400; AAP21208.1; -; mRNA.
DR EMBL; AY087219; AAM64775.1; -; mRNA.
DR PIR; T47538; T47538.
DR RefSeq; NP_190184.1; NM_114467.4.
DR AlphaFoldDB; O23629; -.
DR SMR; O23629; -.
DR BioGRID; 9061; 1.
DR IntAct; O23629; 1.
DR STRING; 3702.AT3G45980.1; -.
DR iPTMnet; O23629; -.
DR PaxDb; O23629; -.
DR PRIDE; O23629; -.
DR ProteomicsDB; 222373; -.
DR EnsemblPlants; AT3G45980.1; AT3G45980.1; AT3G45980.
DR GeneID; 823741; -.
DR Gramene; AT3G45980.1; AT3G45980.1; AT3G45980.
DR KEGG; ath:AT3G45980; -.
DR Araport; AT3G45980; -.
DR TAIR; locus:2077182; AT3G45980.
DR eggNOG; KOG1744; Eukaryota.
DR HOGENOM; CLU_075666_1_0_1; -.
DR InParanoid; O23629; -.
DR OMA; WANMEAQ; -.
DR OrthoDB; 1536672at2759; -.
DR PhylomeDB; O23629; -.
DR PRO; PR:O23629; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; O23629; baseline and differential.
DR Genevisible; O23629; AT.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0009534; C:chloroplast thylakoid; HDA:TAIR.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005730; C:nucleolus; HDA:TAIR.
DR GO; GO:0000786; C:nucleosome; IEA:UniProtKB-KW.
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:0000305"
FT CHAIN 2..150
FT /note="Histone H2B.6"
FT /id="PRO_0000238693"
FT REGION 1..58
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 2
FT /note="N,N,N-trimethylalanine; alternate"
FT /evidence="ECO:0000269|PubMed:17691833"
FT MOD_RES 2
FT /note="N,N-dimethylalanine; alternate"
FT /evidence="ECO:0000269|PubMed:17691833"
FT MOD_RES 2
FT /note="N-methylalanine; alternate"
FT /evidence="ECO:0000269|PubMed:17691833"
FT MOD_RES 7
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000269|PubMed:17691833"
FT MOD_RES 12
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000269|PubMed:17691833"
FT MOD_RES 13
FT /note="N6,N6-dimethyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q9FFC0"
FT MOD_RES 28
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000269|PubMed:17691833"
FT MOD_RES 33
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000269|PubMed:17691833"
FT MOD_RES 39
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000269|PubMed:17691833"
FT MOD_RES 40
FT /note="N6-acetyllysine; partial"
FT /evidence="ECO:0000269|PubMed:17691833"
FT CROSSLNK 146
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000250|UniProtKB:Q9LQQ4"
SQ SEQUENCE 150 AA; 16436 MW; E7693DD90DEB994B CRC64;
MAPRAEKKPA EKKPAAEKPV EEKSKAEKAP AEKKPKAGKK LPKEAGAGGD KKKKMKKKSV
ETYKIYIFKV LKQVHPDIGI SSKAMGIMNS FINDIFEKLA SESSKLARYN KKPTITSREI
QTAVRLVLPG ELAKHAVSEG TKAVTKFTSS
