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Protein

Histone H2B 5

Gene

H2B-V

Organism
Gallus gallus (Chicken)
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.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiR-GGA-171306. Packaging Of Telomere Ends.
R-GGA-212300. PRC2 methylates histones and DNA.
R-GGA-2299718. Condensation of Prophase Chromosomes.
R-GGA-2559580. Oxidative Stress Induced Senescence.
R-GGA-2559582. Senescence-Associated Secretory Phenotype (SASP).
R-GGA-2559586. DNA Damage/Telomere Stress Induced Senescence.
R-GGA-3214847. HATs acetylate histones.
R-GGA-427359. SIRT1 negatively regulates rRNA Expression.
R-GGA-5250924. B-WICH complex positively regulates rRNA expression.
R-GGA-5578749. Transcriptional regulation by small RNAs.
R-GGA-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
R-GGA-5693571. Nonhomologous End-Joining (NHEJ).
R-GGA-5693607. Processing of DNA double-strand break ends.
R-GGA-606279. Deposition of new CENPA-containing nucleosomes at the centromere.
R-GGA-69473. G2/M DNA damage checkpoint.
R-GGA-73728. RNA Polymerase I Promoter Opening.
R-GGA-73777. RNA Polymerase I Chain Elongation.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H2B 5
Alternative name(s):
H2B V
Gene namesi
Name:H2B-V
OrganismiGallus gallus (Chicken)
Taxonomic identifieri9031 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiArchelosauriaArchosauriaDinosauriaSaurischiaTheropodaCoelurosauriaAvesNeognathaeGalloanseraeGalliformesPhasianidaePhasianinaeGallus
Proteomesi
  • UP000000539 Componenti: Chromosome 1

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 5PRO_0000244864Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei6 – 61N6-acetyllysine1 Publication
Modified residuei13 – 131N6-acetyllysine1 Publication
Modified residuei15 – 151Phosphoserine1 Publication
Modified residuei16 – 161N6-acetyllysine1 Publication
Modified residuei21 – 211N6-acetyllysine1 Publication
Glycosylationi113 – 1131O-linked (GlcNAc)By similarity
Cross-linki121 – 121Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication

Post-translational modificationi

Monoubiquitination of Lys-121 by the BRE1 gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 'Lys-4' and 'Lys-79' methylation.By similarity
Phosphorylated on Ser-15 during apoptosis; which facilitates apoptotic chromatin condensation.1 Publication
GlcNAcylation at Ser-113 promotes monoubiquitination of Lys-121. It fluctuates in response to extracellular glucose, and associates with transcribed genes (By similarity).By similarity

Keywords - PTMi

Acetylation, Glycoprotein, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiP0C1H4.

PTM databases

iPTMnetiP0C1H4.

Expressioni

Gene expression databases

ExpressionAtlasiP0C1H4. baseline.

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

STRINGi9031.ENSGALP00000037260.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2XQLelectron microscopy19.50B/D/F/H/J37-126[»]
ProteinModelPortaliP0C1H4.
SMRiP0C1H4. Positions 5-126.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0C1H4.

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H2B family.Curated

Phylogenomic databases

eggNOGiKOG1744. Eukaryota.
ENOG4111NV5. LUCA.
GeneTreeiENSGT00760000118976.
HOGENOMiHOG000231213.
HOVERGENiHBG007774.
InParanoidiP0C1H4.
KOiK11252.
OMAiKATHLPR.
OrthoDBiEOG72VH8J.
PhylomeDBiP0C1H4.
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.

P0C1H4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPEPAKSAPA PKKGSKKAVT KTQKKGDKKR RKSRKESYSI YVYKVLKQVH
60 70 80 90 100
PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRSTI TSREIQTAVR
110 120
LLLPGELAKH AVSEGTKAVT KYTSSK
Length:126
Mass (Da):13,950
Last modified:January 23, 2007 - v2
Checksum:i44A941FE24F77015
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M57901 Genomic DNA. Translation: AAA48792.1.
PIRiJH0362.
RefSeqiNP_001073189.1. NM_001079721.1.
UniGeneiGga.40038.

Genome annotation databases

EnsembliENSGALT00000038052; ENSGALP00000037260; ENSGALG00000027382.
GeneIDi417957.
KEGGigga:417957.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M57901 Genomic DNA. Translation: AAA48792.1.
PIRiJH0362.
RefSeqiNP_001073189.1. NM_001079721.1.
UniGeneiGga.40038.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2XQLelectron microscopy19.50B/D/F/H/J37-126[»]
ProteinModelPortaliP0C1H4.
SMRiP0C1H4. Positions 5-126.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9031.ENSGALP00000037260.

PTM databases

iPTMnetiP0C1H4.

Proteomic databases

PaxDbiP0C1H4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSGALT00000038052; ENSGALP00000037260; ENSGALG00000027382.
GeneIDi417957.
KEGGigga:417957.

Organism-specific databases

CTDi417957.

Phylogenomic databases

eggNOGiKOG1744. Eukaryota.
ENOG4111NV5. LUCA.
GeneTreeiENSGT00760000118976.
HOGENOMiHOG000231213.
HOVERGENiHBG007774.
InParanoidiP0C1H4.
KOiK11252.
OMAiKATHLPR.
OrthoDBiEOG72VH8J.
PhylomeDBiP0C1H4.
TreeFamiTF300212.

Enzyme and pathway databases

ReactomeiR-GGA-171306. Packaging Of Telomere Ends.
R-GGA-212300. PRC2 methylates histones and DNA.
R-GGA-2299718. Condensation of Prophase Chromosomes.
R-GGA-2559580. Oxidative Stress Induced Senescence.
R-GGA-2559582. Senescence-Associated Secretory Phenotype (SASP).
R-GGA-2559586. DNA Damage/Telomere Stress Induced Senescence.
R-GGA-3214847. HATs acetylate histones.
R-GGA-427359. SIRT1 negatively regulates rRNA Expression.
R-GGA-5250924. B-WICH complex positively regulates rRNA expression.
R-GGA-5578749. Transcriptional regulation by small RNAs.
R-GGA-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
R-GGA-5693571. Nonhomologous End-Joining (NHEJ).
R-GGA-5693607. Processing of DNA double-strand break ends.
R-GGA-606279. Deposition of new CENPA-containing nucleosomes at the centromere.
R-GGA-69473. G2/M DNA damage checkpoint.
R-GGA-73728. RNA Polymerase I Promoter Opening.
R-GGA-73777. RNA Polymerase I Chain Elongation.

Miscellaneous databases

EvolutionaryTraceiP0C1H4.
PROiP0C1H4.

Gene expression databases

ExpressionAtlasiP0C1H4. baseline.

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

  1. "Nucleotide sequence of a member of the chicken H2B histone-encoding gene family."
    Nakayama T., Setoguchi Y.
    Gene 98:299-300(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: White leghorn.
  2. "Organization of the chicken histone genes in a major gene cluster and generation of an almost complete set of the core histone protein sequences."
    Takami Y., Higashio M., Fukuoka T., Takechi S., Nakayama T.
    DNA Res. 3:95-99(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], NOMENCLATURE.
    Strain: White leghorn.
  3. "Ubiquitinated histone H2B is preferentially located in transcriptionally active chromatin."
    Nickel B.E., Allis C.D., Davie J.R.
    Biochemistry 28:958-963(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION.
  4. "Apoptotic phosphorylation of histone H2B is mediated by mammalian sterile twenty kinase."
    Cheung W.L., Ajiro K., Samejima K., Kloc M., Cheung P., Mizzen C.A., Beeser A., Etkin L.D., Chernoff J., Earnshaw W.C., Allis C.D.
    Cell 113:507-517(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION AT SER-15.
  5. "Acetylation of histone H2B mirrors that of H4 and H3 at the chicken beta-globin locus but not at housekeeping genes."
    Myers F.A., Chong W., Evans D.R., Thorne A.W., Crane-Robinson C.
    J. Biol. Chem. 278:36315-36322(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION AT LYS-6; LYS-13; LYS-16 AND LYS-21.

Entry informationi

Entry nameiH2B5_CHICK
AccessioniPrimary (citable) accession number: P0C1H4
Secondary accession number(s): P02279
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 11, 2006
Last sequence update: January 23, 2007
Last modified: June 8, 2016
This is version 79 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.