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Protein

Histone H2B.6

Gene

H2B

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H2B.6
Alternative name(s):
H2BAt
HTB9
Gene namesi
Name:H2B
Ordered Locus Names:At3g45980
ORF Names:F16L2.190
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 3

Organism-specific databases

TAIRiAT3G45980.

Subcellular locationi

GO - Cellular componenti

  • chloroplast stroma Source: TAIR
  • chloroplast thylakoid Source: TAIR
  • nuclear nucleosome Source: GO_Central
  • nucleolus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved
Chaini2 – 150149Histone H2B.6PRO_0000238693Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N,N,N-trimethylalanine; alternate1 Publication
Modified residuei2 – 21N,N-dimethylalanine; alternate1 Publication
Modified residuei2 – 21N-methylalanine; alternate1 Publication
Modified residuei7 – 71N6-acetyllysine1 Publication
Modified residuei12 – 121N6-acetyllysine1 Publication
Modified residuei13 – 131N6,N6-dimethyllysineBy similarity
Modified residuei28 – 281N6-acetyllysine1 Publication
Modified residuei33 – 331N6-acetyllysine1 Publication
Modified residuei39 – 391N6-acetyllysine1 Publication
Modified residuei40 – 401N6-acetyllysine; partial1 Publication
Cross-linki146 – 146Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity

Post-translational modificationi

Can be acetylated to form H2BK6ac, H2BK11ac, H2BK22ac, H2BK27ac H2BK33ac and H2BK34ac.1 Publication
Mono-, di- or trimethylated at the N-terminus to form H2BA1me1/2/3. H2BA1me2 may be acetylated to form H2BA1me2K6ac and H2BA1me2K6acK11ac.1 Publication
Monoubiquitinated by BRE1 to form H2BK143ub1 and deubiquitinated by UBP26. Required for heterochromatic histone H3 di- and trimethylation at H3K4me. May give a specific tag for epigenetic transcriptional activation.

Keywords - PTMi

Acetylation, Isopeptide bond, Methylation, Ubl conjugation

Proteomic databases

PaxDbiO23629.
PRIDEiO23629.

PTM databases

iPTMnetiO23629.

Expressioni

Developmental stagei

Strong up-regulation during the S-phase.1 Publication

Gene expression databases

ExpressionAtlasiO23629. baseline and differential.
GenevisibleiO23629. AT.

Interactioni

Subunit structurei

The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.

Protein-protein interaction databases

BioGridi9061. 1 interaction.
IntActiO23629. 1 interaction.
STRINGi3702.AT3G45980.1.

Structurei

3D structure databases

ProteinModelPortaliO23629.
SMRiO23629. Positions 26-150.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H2B family.Curated

Phylogenomic databases

eggNOGiKOG1744. Eukaryota.
ENOG4111NV5. LUCA.
HOGENOMiHOG000231213.
InParanoidiO23629.
KOiK11252.
OMAiTGDKKHK.
PhylomeDBiO23629.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_H2A/H2B/H3.
IPR000558. Histone_H2B.
[Graphical view]
PANTHERiPTHR23428. PTHR23428. 1 hit.
PfamiPF00125. Histone. 1 hit.
[Graphical view]
PRINTSiPR00621. HISTONEH2B.
SMARTiSM00427. H2B. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00357. HISTONE_H2B. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

O23629-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAPRAEKKPA EKKPAAEKPV EEKSKAEKAP AEKKPKAGKK LPKEAGAGGD
60 70 80 90 100
KKKKMKKKSV ETYKIYIFKV LKQVHPDIGI SSKAMGIMNS FINDIFEKLA
110 120 130 140 150
SESSKLARYN KKPTITSREI QTAVRLVLPG ELAKHAVSEG TKAVTKFTSS
Length:150
Mass (Da):16,436
Last modified:January 23, 2007 - v3
Checksum:iE7693DD90DEB994B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y12576 mRNA. Translation: CAA73156.1.
AL162459 Genomic DNA. Translation: CAB82822.1.
CP002686 Genomic DNA. Translation: AEE78097.1.
BT006400 mRNA. Translation: AAP21208.1.
AY087219 mRNA. Translation: AAM64775.1.
PIRiT47538.
RefSeqiNP_190184.1. NM_114467.4.
UniGeneiAt.4757.
At.71080.

Genome annotation databases

EnsemblPlantsiAT3G45980.1; AT3G45980.1; AT3G45980.
GeneIDi823741.
GrameneiAT3G45980.1; AT3G45980.1; AT3G45980.
KEGGiath:AT3G45980.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y12576 mRNA. Translation: CAA73156.1.
AL162459 Genomic DNA. Translation: CAB82822.1.
CP002686 Genomic DNA. Translation: AEE78097.1.
BT006400 mRNA. Translation: AAP21208.1.
AY087219 mRNA. Translation: AAM64775.1.
PIRiT47538.
RefSeqiNP_190184.1. NM_114467.4.
UniGeneiAt.4757.
At.71080.

3D structure databases

ProteinModelPortaliO23629.
SMRiO23629. Positions 26-150.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi9061. 1 interaction.
IntActiO23629. 1 interaction.
STRINGi3702.AT3G45980.1.

PTM databases

iPTMnetiO23629.

Proteomic databases

PaxDbiO23629.
PRIDEiO23629.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT3G45980.1; AT3G45980.1; AT3G45980.
GeneIDi823741.
GrameneiAT3G45980.1; AT3G45980.1; AT3G45980.
KEGGiath:AT3G45980.

Organism-specific databases

TAIRiAT3G45980.

Phylogenomic databases

eggNOGiKOG1744. Eukaryota.
ENOG4111NV5. LUCA.
HOGENOMiHOG000231213.
InParanoidiO23629.
KOiK11252.
OMAiTGDKKHK.
PhylomeDBiO23629.

Miscellaneous databases

PROiO23629.

Gene expression databases

ExpressionAtlasiO23629. baseline and differential.
GenevisibleiO23629. AT.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_H2A/H2B/H3.
IPR000558. Histone_H2B.
[Graphical view]
PANTHERiPTHR23428. PTHR23428. 1 hit.
PfamiPF00125. Histone. 1 hit.
[Graphical view]
PRINTSiPR00621. HISTONEH2B.
SMARTiSM00427. H2B. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00357. HISTONE_H2B. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Identification of proliferation-induced genes in Arabidopsis thaliana. Characterization of a new member of the highly evolutionarily conserved histone H2A.F/Z variant subfamily."
    Callard D., Mazzolini L.
    Plant Physiol. 115:1385-1395(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], DEVELOPMENTAL STAGE.
  2. "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana."
    Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B., Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V., Choisne N., Artiguenave F.
    , Robert C., Brottier P., Wincker P., Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H., Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J., Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B., Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D., de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E., Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G., Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J., Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.
    Nature 408:820-822(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  5. "Full-length cDNA from Arabidopsis thaliana."
    Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
    Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  6. "Control of DNA methylation and heterochromatic silencing by histone H2B deubiquitination."
    Sridhar V.V., Kapoor A., Zhang K., Zhu J., Zhou T., Hasegawa P.M., Bressan R.A., Zhu J.-K.
    Nature 447:735-738(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION AT LYS-146, IDENTIFICATION BY MASS SPECTROMETRY.
  7. "Characterization of post-translational modifications of histone H2B-variants isolated from Arabidopsis thaliana."
    Bergmueller E., Gehrig P.M., Gruissem W.
    J. Proteome Res. 6:3655-3668(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION AT LYS-7; LYS-12; LYS-28; LYS-33; LYS-39 AND LYS-40, METHYLATION AT ALA-2, UBIQUITINATION AT LYS-146, IDENTIFICATION BY MASS SPECTROMETRY.

Entry informationi

Entry nameiH2B6_ARATH
AccessioniPrimary (citable) accession number: O23629
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2006
Last sequence update: January 23, 2007
Last modified: July 6, 2016
This is version 115 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Caution

To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2BA1me1/2/3 = mono-, di- and trimethylated Ala-2; H2BK6ac = acetylated Lys-7; H2BK11ac = acetylated Lys-12; H2BK22ac = acetylated Lys-28; H2BK27ac = acetylated Lys-33; H2BK33ac = acetylated Lys-39; H2BK34ac = acetylated Lys-40; H2BK143ub1 = monoubiquitinated Lys-146.Curated

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.