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Protein

Histone H2B type 1

Gene
N/A
Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 4 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.
Has broad antibacterial activity. May contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Antibiotic, Antimicrobial

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H2B type 1
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
ProteomesiUP000002494 Componenti: Unplaced

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11RemovedBy similarity
Chaini2 – 125124Histone H2B type 1PRO_0000071841Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylprolineBy similarity
Modified residuei6 – 61N6-acetyllysine; alternate1 Publication
Modified residuei6 – 61N6-crotonyllysine; alternateBy similarity
Modified residuei12 – 121N6-acetyllysine; alternateBy similarity
Modified residuei12 – 121N6-crotonyllysine; alternateBy similarity
Modified residuei13 – 131N6-acetyllysine; alternate1 Publication
Modified residuei13 – 131N6-crotonyllysine; alternateBy similarity
Modified residuei15 – 151Phosphoserine; by STK4/MST1By similarity
Modified residuei16 – 161N6-acetyllysine; alternate1 Publication
Modified residuei16 – 161N6-crotonyllysine; alternateBy similarity
Modified residuei17 – 171N6-acetyllysine; alternateBy similarity
Modified residuei17 – 171N6-crotonyllysine; alternateBy similarity
Modified residuei21 – 211N6-acetyllysine; alternate1 Publication
Modified residuei21 – 211N6-crotonyllysine; alternateBy similarity
Modified residuei24 – 241N6-acetyllysine; alternateBy similarity
Modified residuei24 – 241N6-crotonyllysine; alternateBy similarity
Modified residuei35 – 351N6-crotonyllysine; alternateBy similarity
Cross-linki35 – 35Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternateBy similarity
Modified residuei37 – 371Phosphoserine; by AMPKBy similarity
Modified residuei47 – 471N6-methyllysineBy similarity
Modified residuei58 – 581N6,N6-dimethyllysineBy similarity
Modified residuei79 – 791Dimethylated arginineBy similarity
Modified residuei85 – 851N6,N6,N6-trimethyllysine; alternateBy similarity
Modified residuei85 – 851N6-acetyllysine; alternateBy similarity
Modified residuei86 – 861Omega-N-methylarginineBy similarity
Modified residuei92 – 921Omega-N-methylarginineBy similarity
Modified residuei108 – 1081N6-methyllysineBy similarity
Modified residuei115 – 1151PhosphothreonineBy similarity
Modified residuei116 – 1161N6-methylated lysineBy similarity
Cross-linki120 – 120Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity

Post-translational modificationi

Monoubiquitination at Lys-35 (H2BK34Ub) by the MSL1/MSL2 dimer is required for histone H3 'Lys-4' (H3K4me) and 'Lys-79' (H3K79me) methylation and transcription activation at specific gene loci, such as HOXA9 and MEIS1 loci. Similarly, monoubiquitination at Lys-120 (H2BK120Ub) by the RNF20/40 complex gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 'Lys-4' and 'Lys-79' methylation. It also functions cooperatively with the FACT dimer to stimulate elongation by RNA polymerase II. H2BK120Ub also acts as a regulator of mRNA splicing: deubiquitination by USP49 is required for efficient cotranscriptional splicing of a large set of exons (By similarity).By similarity
Phosphorylated on Ser-15 (H2BS14ph) by STK4/MST1 during apoptosis; which facilitates apoptotic chromatin condensation. Also phosphorylated on Ser-15 in response to DNA double strand breaks (DSBs), and in correlation with somatic hypermutation and immunoglobulin class-switch recombination. Phosphorylation at Ser-37 (H2BS36ph) by AMPK in response to stress promotes transcription (By similarity).By similarity
Crotonylation (Kcr) is specifically present in male germ cells and marks testis-specific genes in post-meiotic cells, including X-linked genes that escape sex chromosome inactivation in haploid cells. Crotonylation marks active promoters and enhancers and confers resistance to transcriptional repressors. It is also associated with post-meiotically activated genes on autosomes (By similarity).By similarity

Keywords - PTMi

Acetylation, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiQ00715.
PRIDEiQ00715.

PTM databases

PhosphoSiteiQ00715.

Expressioni

Gene expression databases

GenevisibleiQ00715. RN.

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

BioGridi249180. 2 interactions.
IntActiQ00715. 1 interaction.
STRINGi10116.ENSRNOP00000067422.

Structurei

3D structure databases

ProteinModelPortaliQ00715.
SMRiQ00715. Positions 5-125.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H2B family.Curated

Phylogenomic databases

eggNOGiNOG289161.
HOGENOMiHOG000231213.
HOVERGENiHBG007774.
KOiK11252.
PhylomeDBiQ00715.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_core_D.
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.

Q00715-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPEPAKSRPA PKKGSKKAVT KAQKKDGKER KRSRKESYSV YVYKVLKQVH
60 70 80 90 100
PDTGISSKAM GIMNSFVNDI FERIAGERRL AHYNKRSTIT SREIQTAVRL
110 120
LLPGELAKHA VSEGTKAVTK YTSSK
Length:125
Mass (Da):13,990
Last modified:January 23, 2007 - v2
Checksum:i43BF1F86A6DA221A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X59961 Genomic DNA. Translation: CAA42585.1.
PIRiB45945.
S26185.
RefSeqiNP_072173.1. NM_022647.1.
UniGeneiRn.112590.

Genome annotation databases

GeneIDi64647.
KEGGirno:64647.
UCSCiRGD:621439. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X59961 Genomic DNA. Translation: CAA42585.1.
PIRiB45945.
S26185.
RefSeqiNP_072173.1. NM_022647.1.
UniGeneiRn.112590.

3D structure databases

ProteinModelPortaliQ00715.
SMRiQ00715. Positions 5-125.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi249180. 2 interactions.
IntActiQ00715. 1 interaction.
STRINGi10116.ENSRNOP00000067422.

PTM databases

PhosphoSiteiQ00715.

Proteomic databases

PaxDbiQ00715.
PRIDEiQ00715.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi64647.
KEGGirno:64647.
UCSCiRGD:621439. rat.

Organism-specific databases

CTDi8340.

Phylogenomic databases

eggNOGiNOG289161.
HOGENOMiHOG000231213.
HOVERGENiHBG007774.
KOiK11252.
PhylomeDBiQ00715.

Miscellaneous databases

NextBioi613637.
PROiQ00715.

Gene expression databases

GenevisibleiQ00715. RN.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_core_D.
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

  1. "Presence of a bi-directional S phase-specific transcription regulatory element in the promoter shared by testis-specific TH2A and TH2B histone genes."
    Huh N.E., Hwang I., Lim K., You K.H., Chae C.-B.
    Nucleic Acids Res. 19:93-98(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: Sprague-Dawley.
  2. "Molecular cloning and differential expression of somatic and testis-specific H2B histone genes during rat spermatogenesis."
    Kim Y.-J., Hwang I., Tres L.L., Kierszenbaum A.L., Chae C.-B.
    Dev. Biol. 124:23-34(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. Lubec G., Kang S.U., Lubec S.
    Submitted (SEP-2007) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 36-44; 48-73 AND 100-108, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: Sprague-Dawley.
    Tissue: Brain.
  4. "Inhibition of core histones acetylation by carcinogenic nickel(II)."
    Golebiowski F., Kasprzak K.S.
    Mol. Cell. Biochem. 279:133-139(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION AT LYS-6; LYS-13; LYS-16 AND LYS-21.

Entry informationi

Entry nameiH2B1_RAT
AccessioniPrimary (citable) accession number: Q00715
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: January 23, 2007
Last modified: June 24, 2015
This is version 114 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.