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Protein

Histone H2B type 3-A

Gene

Hist3h2ba

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -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.

Miscellaneous

The human orthologous protein seems not to exist.

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding

Enzyme and pathway databases

ReactomeiR-MMU-1221633. Meiotic Synapsis.
R-MMU-201722. Formation of the beta-catenin:TCF transactivating complex.
R-MMU-212300. PRC2 methylates histones and DNA.
R-MMU-2299718. Condensation of Prophase Chromosomes.
R-MMU-2559580. Oxidative Stress Induced Senescence.
R-MMU-2559582. Senescence-Associated Secretory Phenotype (SASP).
R-MMU-2559586. DNA Damage/Telomere Stress Induced Senescence.
R-MMU-3214847. HATs acetylate histones.
R-MMU-427359. SIRT1 negatively regulates rRNA expression.
R-MMU-427413. NoRC negatively regulates rRNA expression.
R-MMU-5250924. B-WICH complex positively regulates rRNA expression.
R-MMU-5578749. Transcriptional regulation by small RNAs.
R-MMU-5625886. Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3.
R-MMU-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
R-MMU-5693571. Nonhomologous End-Joining (NHEJ).
R-MMU-5693607. Processing of DNA double-strand break ends.
R-MMU-573389. NoRC negatively regulates rRNA expression.
R-MMU-69473. G2/M DNA damage checkpoint.
R-MMU-73728. RNA Polymerase I Promoter Opening.
R-MMU-73777. RNA Polymerase I Chain Elongation.
R-MMU-8936459. RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function.
R-MMU-8939236. RUNX1 regulates transcription of genes involved in differentiation of HSCs.
R-MMU-912497. Meiotic Recombination.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H2B type 3-A
Gene namesi
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 11

Organism-specific databases

MGIiMGI:1925553. Hist3h2ba.

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00002448372 – 126Histone H2B type 3-AAdd BLAST125

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylprolineBy similarity1
Modified residuei12N6-(beta-hydroxybutyryl)lysine; alternate1 Publication1
Modified residuei12N6-acetyllysine; alternateBy similarity1
Modified residuei12N6-crotonyllysine; alternate1 Publication1
Modified residuei13N6-(2-hydroxyisobutyryl)lysine; alternate1 Publication1
Modified residuei13N6-acetyllysine; alternateBy similarity1
Modified residuei13N6-crotonyllysine; alternate1 Publication1
Modified residuei15Phosphoserine; by STK4/MST12 Publications1
Modified residuei16N6-acetyllysine; alternateBy similarity1
Modified residuei16N6-crotonyllysine; alternate1 Publication1
Modified residuei17N6-acetyllysine; alternateBy similarity1
Modified residuei17N6-crotonyllysine; alternate1 Publication1
Modified residuei21N6-(2-hydroxyisobutyryl)lysine; alternate1 Publication1
Modified residuei21N6-(beta-hydroxybutyryl)lysine; alternate1 Publication1
Modified residuei21N6-acetyllysine; alternateBy similarity1
Modified residuei21N6-butyryllysine; alternateBy similarity1
Modified residuei21N6-crotonyllysine; alternate1 Publication1
Cross-linki21Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateBy similarity
Modified residuei24N6-(2-hydroxyisobutyryl)lysine; alternate1 Publication1
Modified residuei24N6-acetyllysine; alternateBy similarity1
Modified residuei24N6-crotonyllysine; alternate1 Publication1
Modified residuei25N6-(2-hydroxyisobutyryl)lysine1 Publication1
Modified residuei35N6-(2-hydroxyisobutyryl)lysine; alternate1 Publication1
Modified residuei35N6-(beta-hydroxybutyryl)lysine; alternate1 Publication1
Modified residuei35N6-crotonyllysine; alternate1 Publication1
Modified residuei35N6-succinyllysine; alternateBy similarity1
Cross-linki35Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternateBy similarity
Modified residuei37Phosphoserine; by AMPK1 Publication1
Modified residuei44N6-(2-hydroxyisobutyryl)lysine1 Publication1
Modified residuei47N6-(2-hydroxyisobutyryl)lysine; alternate1 Publication1
Modified residuei47N6-methyllysine; alternateBy similarity1
Modified residuei58N6,N6-dimethyllysine; alternateBy similarity1
Modified residuei58N6-(2-hydroxyisobutyryl)lysine; alternate1 Publication1
Modified residuei80Dimethylated arginineBy similarity1
Modified residuei86N6,N6,N6-trimethyllysine; alternateBy similarity1
Modified residuei86N6-(2-hydroxyisobutyryl)lysine; alternate1 Publication1
Modified residuei86N6-acetyllysine; alternateBy similarity1
Modified residuei87Omega-N-methylarginineBy similarity1
Modified residuei93Omega-N-methylarginineBy similarity1
Modified residuei109N6-(2-hydroxyisobutyryl)lysine; alternate1 Publication1
Modified residuei109N6-(beta-hydroxybutyryl)lysine; alternate1 Publication1
Modified residuei109N6-methyllysine; alternateBy similarity1
Modified residuei116PhosphothreonineBy similarity1
Modified residuei117N6-(2-hydroxyisobutyryl)lysine; alternate1 Publication1
Modified residuei117N6-(beta-hydroxybutyryl)lysine; alternate1 Publication1
Modified residuei117N6-methylated lysine; alternateBy similarity1
Modified residuei117N6-succinyllysine; alternateBy similarity1
Modified residuei121N6-(2-hydroxyisobutyryl)lysine; alternate1 Publication1
Modified residuei121N6-succinyllysine; alternate1 Publication1
Cross-linki121Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternateBy 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-121 (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.3 Publications
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.1 Publication
Hydroxybutyrylation of histones is induced by starvation.1 Publication

Keywords - PTMi

Acetylation, Hydroxylation, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ9D2U9.
MaxQBiQ9D2U9.
PaxDbiQ9D2U9.
PeptideAtlasiQ9D2U9.
PRIDEiQ9D2U9.

PTM databases

iPTMnetiQ9D2U9.
PhosphoSitePlusiQ9D2U9.

Expressioni

Gene expression databases

BgeeiENSMUSG00000056895.
CleanExiMM_HIST3H2BA.
GenevisibleiQ9D2U9. MM.

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.1 Publication

GO - Molecular functioni

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000076397.

Structurei

Secondary structure

1126
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi39 – 49Combined sources11
Helixi57 – 84Combined sources28
Beta strandi88 – 90Combined sources3
Helixi92 – 102Combined sources11
Helixi106 – 123Combined sources18

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1U35X-ray3.00D/H1-126[»]
2F8NX-ray2.90D1-126[»]
5B1LX-ray2.35D/H1-126[»]
5B1MX-ray2.34D/H1-126[»]
ProteinModelPortaliQ9D2U9.
SMRiQ9D2U9.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9D2U9.

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H2B family.Curated

Phylogenomic databases

eggNOGiKOG1744. Eukaryota.
ENOG4111NV5. LUCA.
GeneTreeiENSGT00760000118976.
HOGENOMiHOG000231213.
HOVERGENiHBG007774.
InParanoidiQ9D2U9.
KOiK11252.
OMAiRYKIANS.
OrthoDBiEOG091G0XGD.
PhylomeDBiQ9D2U9.
TreeFamiTF300212.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiView protein in InterPro
IPR009072. Histone-fold.
IPR007125. Histone_H2A/H2B/H3.
IPR000558. Histone_H2B.
PANTHERiPTHR23428. PTHR23428. 1 hit.
PfamiView protein in Pfam
PF00125. Histone. 1 hit.
PRINTSiPR00621. HISTONEH2B.
SMARTiView protein in SMART
SM00427. H2B. 1 hit.
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiView protein in PROSITE
PS00357. HISTONE_H2B. 1 hit.

Sequencei

Sequence statusi: Complete.

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

Q9D2U9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPEPSRSTPA PKKGSKKAIT KAQKKDGKKR KRGRKESYSI YVYKVLKQVH
60 70 80 90 100
PDTGISSKAM GIMNSFVNDI FERIASEASR LAHYNKRSTI TSREVQTAVR
110 120
LLLPGELAKH AVSEGTKAVT KYTSSK
Length:126
Mass (Da):13,994
Last modified:January 23, 2007 - v3
Checksum:iDC1CF72D9457CC56
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY158942 Genomic DNA. Translation: AAO06252.1.
AK018765 mRNA. Translation: BAB31395.1.
BC051921 mRNA. Translation: AAH51921.1.
CCDSiCCDS24754.1.
RefSeqiNP_084358.1. NM_030082.4.
UniGeneiMm.28022.

Genome annotation databases

EnsembliENSMUST00000078267; ENSMUSP00000076397; ENSMUSG00000056895.
GeneIDi78303.
KEGGimmu:78303.
UCSCiuc007jcr.2. mouse.

Similar proteinsi

Entry informationi

Entry nameiH2B3A_MOUSE
AccessioniPrimary (citable) accession number: Q9D2U9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 11, 2006
Last sequence update: January 23, 2007
Last modified: March 28, 2018
This is version 142 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome