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Protein

Histone H2B type 3-A

Gene

Hist3h2ba

Organism
Mus musculus (Mouse)
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

Complete GO annotation...

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiR-MMU-1221633. Meiotic Synapsis.
R-MMU-3214847. HATs acetylate histones.
R-MMU-573389. NoRC negatively regulates rRNA expression.
R-MMU-912497. Meiotic Recombination.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H2B type 3-A
Gene namesi
Name:Hist3h2ba
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 11

Organism-specific databases

MGIiMGI:1925553. Hist3h2ba.

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 methionineiRemovedBy similarity
Chaini2 – 126125Histone H2B type 3-APRO_0000244837Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylprolineBy similarity
Modified residuei12 – 121N6-acetyllysine; alternateBy similarity
Modified residuei12 – 121N6-crotonyllysine; alternate1 Publication
Modified residuei13 – 131N6-acetyllysine; alternateBy similarity
Modified residuei13 – 131N6-crotonyllysine; alternate1 Publication
Modified residuei15 – 151Phosphoserine; by STK4/MST12 Publications
Modified residuei16 – 161N6-acetyllysine; alternateBy similarity
Modified residuei16 – 161N6-crotonyllysine; alternate1 Publication
Modified residuei17 – 171N6-acetyllysine; alternateBy similarity
Modified residuei17 – 171N6-crotonyllysine; alternate1 Publication
Modified residuei21 – 211N6-acetyllysine; alternateBy similarity
Modified residuei21 – 211N6-crotonyllysine; alternate1 Publication
Modified residuei24 – 241N6-acetyllysine; alternateBy similarity
Modified residuei24 – 241N6-crotonyllysine; alternate1 Publication
Modified residuei35 – 351N6-crotonyllysine; alternate1 Publication
Cross-linki35 – 35Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternateBy similarity
Modified residuei37 – 371Phosphoserine; by AMPK1 Publication
Modified residuei47 – 471N6-methyllysineBy similarity
Modified residuei58 – 581N6,N6-dimethyllysineBy similarity
Modified residuei80 – 801Dimethylated arginineBy similarity
Modified residuei86 – 861N6,N6,N6-trimethyllysine; alternateBy similarity
Modified residuei86 – 861N6-acetyllysine; alternateBy similarity
Modified residuei87 – 871Omega-N-methylarginineBy similarity
Modified residuei93 – 931Omega-N-methylarginineBy similarity
Modified residuei109 – 1091N6-methyllysineBy similarity
Modified residuei116 – 1161PhosphothreonineBy similarity
Modified residuei117 – 1171N6-methylated lysineBy similarity
Cross-linki121 – 121Glycyl 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-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

Keywords - PTMi

Acetylation, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ9D2U9.
MaxQBiQ9D2U9.
PaxDbiQ9D2U9.
PRIDEiQ9D2U9.

PTM databases

iPTMnetiQ9D2U9.
PhosphoSiteiQ9D2U9.

Expressioni

Gene expression databases

BgeeiQ9D2U9.
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

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000076397.

Structurei

Secondary structure

1
126
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi39 – 4911Combined sources
Helixi57 – 8428Combined sources
Beta strandi88 – 903Combined sources
Helixi92 – 10211Combined sources
Helixi105 – 12218Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1U35X-ray3.00D/H1-126[»]
2F8NX-ray2.90D1-126[»]
ProteinModelPortaliQ9D2U9.
SMRiQ9D2U9. Positions 5-126.
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.
OMAiHCCSSEP.
OrthoDBiEOG72VH8J.
PhylomeDBiQ9D2U9.
TreeFamiTF300212.

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.

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.

Cross-referencesi

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.

3D structure databases

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

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000076397.

PTM databases

iPTMnetiQ9D2U9.
PhosphoSiteiQ9D2U9.

Proteomic databases

EPDiQ9D2U9.
MaxQBiQ9D2U9.
PaxDbiQ9D2U9.
PRIDEiQ9D2U9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi337872.
MGIiMGI:1925553. Hist3h2ba.

Phylogenomic databases

eggNOGiKOG1744. Eukaryota.
ENOG4111NV5. LUCA.
GeneTreeiENSGT00760000118976.
HOGENOMiHOG000231213.
HOVERGENiHBG007774.
InParanoidiQ9D2U9.
KOiK11252.
OMAiHCCSSEP.
OrthoDBiEOG72VH8J.
PhylomeDBiQ9D2U9.
TreeFamiTF300212.

Enzyme and pathway databases

ReactomeiR-MMU-1221633. Meiotic Synapsis.
R-MMU-3214847. HATs acetylate histones.
R-MMU-573389. NoRC negatively regulates rRNA expression.
R-MMU-912497. Meiotic Recombination.

Miscellaneous databases

EvolutionaryTraceiQ9D2U9.
NextBioi348649.
PROiQ9D2U9.
SOURCEiSearch...

Gene expression databases

BgeeiQ9D2U9.
CleanExiMM_HIST3H2BA.
GenevisibleiQ9D2U9. MM.

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. "The human and mouse replication-dependent histone genes."
    Marzluff W.F., Gongidi P., Woods K.R., Jin J., Maltais L.J.
    Genomics 80:487-498(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Cerebellum.
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Brain.
  4. "Phosphorylation of histone H2B at DNA double-strand breaks."
    Fernandez-Capetillo O., Allis C.D., Nussenzweig A.
    J. Exp. Med. 199:1671-1677(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION AT SER-15.
  5. "Histone modifications associated with somatic hypermutation."
    Odegard V.H., Kim S.T., Anderson S.M., Shlomchik M.J., Schatz D.G.
    Immunity 23:101-110(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION AT SER-15.
  6. "Signaling kinase AMPK activates stress-promoted transcription via histone H2B phosphorylation."
    Bungard D., Fuerth B.J., Zeng P.Y., Faubert B., Maas N.L., Viollet B., Carling D., Thompson C.B., Jones R.G., Berger S.L.
    Science 329:1201-1205(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION AT SER-37.
  7. "Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification."
    Tan M., Luo H., Lee S., Jin F., Yang J.S., Montellier E., Buchou T., Cheng Z., Rousseaux S., Rajagopal N., Lu Z., Ye Z., Zhu Q., Wysocka J., Ye Y., Khochbin S., Ren B., Zhao Y.
    Cell 146:1016-1028(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: CROTONYLATION AT LYS-12; LYS-13; LYS-16; LYS-17; LYS-21; LYS-24 AND LYS-35.
  8. Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) IN COMPLEX WITH THE NUCLEOSOME CORE PARTICLE.

Entry informationi

Entry nameiH2B3A_MOUSE
AccessioniPrimary (citable) accession number: Q9D2U9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 11, 2006
Last sequence update: January 23, 2007
Last modified: May 11, 2016
This is version 126 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Miscellaneous

The human orthologous protein seems not to exist.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.