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Protein

Histone H3.1

Gene
N/A
Organism
Rattus norvegicus (Rat)
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

Enzyme and pathway databases

ReactomeiR-RNO-212300. PRC2 methylates histones and DNA.
R-RNO-2559580. Oxidative Stress Induced Senescence.
R-RNO-2559582. Senescence-Associated Secretory Phenotype (SASP).
R-RNO-3214841. PKMTs methylate histone lysines.
R-RNO-3214842. HDMs demethylate histones.
R-RNO-3214847. HATs acetylate histones.
R-RNO-3214858. RMTs methylate histone arginines.
R-RNO-3247509. Chromatin modifying enzymes.
R-RNO-427359. SIRT1 negatively regulates rRNA Expression.
R-RNO-427413. NoRC negatively regulates rRNA expression.
R-RNO-5250924. B-WICH complex positively regulates rRNA expression.
R-RNO-5578749. Transcriptional regulation by small RNAs.
R-RNO-5625886. Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3.
R-RNO-73728. RNA Polymerase I Promoter Opening.
R-RNO-73777. RNA Polymerase I Chain Elongation.
R-RNO-983231. Factors involved in megakaryocyte development and platelet production.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H3.1
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 17

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 – 136135Histone H3.1PRO_0000253949Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei3 – 31Asymmetric dimethylarginine; by PRMT6; alternateBy similarity
Modified residuei3 – 31Citrulline; alternateBy similarity
Modified residuei4 – 41Phosphothreonine; by GSG2By similarity
Modified residuei5 – 51Allysine; alternateBy similarity
Modified residuei5 – 51N6,N6,N6-trimethyllysine; alternateBy similarity
Modified residuei5 – 51N6,N6-dimethyllysine; alternateBy similarity
Modified residuei5 – 51N6-acetyllysine; alternateBy similarity
Modified residuei5 – 51N6-crotonyllysine; alternateBy similarity
Modified residuei5 – 51N6-methyllysine; alternateBy similarity
Modified residuei7 – 71Phosphothreonine; by PKCBy similarity
Modified residuei9 – 91Citrulline; alternateBy similarity
Modified residuei9 – 91Symmetric dimethylarginine; by PRMT5; alternateBy similarity
Modified residuei10 – 101N6,N6,N6-trimethyllysine; alternateBy similarity
Modified residuei10 – 101N6,N6-dimethyllysine; alternateBy similarity
Modified residuei10 – 101N6-acetyllysine; alternateBy similarity
Modified residuei10 – 101N6-crotonyllysine; alternateBy similarity
Modified residuei10 – 101N6-methyllysine; alternateBy similarity
Modified residuei11 – 111Phosphoserine; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA51 Publication
Modified residuei12 – 121Phosphothreonine; by PKC and CHEK11 Publication
Modified residuei15 – 151N6-acetyllysineBy similarity
Modified residuei18 – 181Asymmetric dimethylarginine; by CARM1; alternateBy similarity
Modified residuei18 – 181Citrulline; alternateBy similarity
Modified residuei19 – 191N6-acetyllysine; alternateBy similarity
Modified residuei19 – 191N6-crotonyllysine; alternateBy similarity
Modified residuei19 – 191N6-methyllysine; alternateBy similarity
Modified residuei24 – 241N6-acetyllysine; alternateBy similarity
Modified residuei24 – 241N6-crotonyllysine; alternateBy similarity
Modified residuei24 – 241N6-methyllysine; alternateBy similarity
Modified residuei27 – 271CitrullineBy similarity
Modified residuei28 – 281N6,N6,N6-trimethyllysine; alternateBy similarity
Modified residuei28 – 281N6,N6-dimethyllysine; alternateBy similarity
Modified residuei28 – 281N6-acetyllysine; alternateBy similarity
Modified residuei28 – 281N6-crotonyllysine; alternateBy similarity
Modified residuei28 – 281N6-methyllysine; alternateBy similarity
Modified residuei29 – 291Phosphoserine; by AURKB, AURKC and RPS6KA5By similarity
Modified residuei37 – 371N6,N6,N6-trimethyllysine; alternateCurated
Modified residuei37 – 371N6,N6-dimethyllysine; alternateBy similarity
Modified residuei37 – 371N6-acetyllysine; alternateBy similarity
Modified residuei37 – 371N6-methyllysine; alternateBy similarity
Modified residuei38 – 381N6-methyllysineBy similarity
Modified residuei42 – 421PhosphotyrosineBy similarity
Modified residuei57 – 571N6,N6,N6-trimethyllysine; alternateBy similarity
Modified residuei57 – 571N6-acetyllysine; alternateBy similarity
Modified residuei57 – 571N6-crotonyllysine; alternateBy similarity
Modified residuei57 – 571N6-methyllysine; by EHMT2; alternateBy similarity
Modified residuei58 – 581PhosphoserineBy similarity
Modified residuei65 – 651N6-methyllysineBy similarity
Modified residuei80 – 801N6,N6,N6-trimethyllysine; alternateBy similarity
Modified residuei80 – 801N6,N6-dimethyllysine; alternateBy similarity
Modified residuei80 – 801N6-acetyllysine; alternateBy similarity
Modified residuei80 – 801N6-methyllysine; alternateBy similarity
Modified residuei81 – 811PhosphothreonineBy similarity
Modified residuei87 – 871PhosphoserineBy similarity
Modified residuei108 – 1081PhosphothreonineBy similarity
Modified residuei116 – 1161N6-acetyllysineBy similarity
Modified residuei123 – 1231N6-acetyllysine; alternateBy similarity
Modified residuei123 – 1231N6-methyllysine; alternateBy similarity

Post-translational modificationi

Acetylation is generally linked to gene activation. Acetylation on Lys-10 (H3K9ac) impairs methylation at Arg-9 (H3R8me2s). Acetylation on Lys-19 (H3K18ac) and Lys-24 (H3K24ac) favors methylation at Arg-18 (H3R17me). Acetylation at Lys-123 (H3K122ac) by EP300/p300 plays a central role in chromatin structure: localizes at the surface of the histone octamer and stimulates transcription, possibly by promoting nucleosome instability (By similarity).By similarity
Citrullination at Arg-9 (H3R8ci) and/or Arg-18 (H3R17ci) by PADI4 impairs methylation and represses transcription.By similarity
Asymmetric dimethylation at Arg-18 (H3R17me2a) by CARM1 is linked to gene activation. Symmetric dimethylation at Arg-9 (H3R8me2s) by PRMT5 is linked to gene repression. Asymmetric dimethylation at Arg-3 (H3R2me2a) by PRMT6 is linked to gene repression and is mutually exclusive with H3 Lys-5 methylation (H3K4me2 and H3K4me3). H3R2me2a is present at the 3' of genes regardless of their transcription state and is enriched on inactive promoters, while it is absent on active promoters (By similarity).By similarity
Methylation at Lys-5 (H3K4me), Lys-37 (H3K36me) and Lys-80 (H3K79me) are linked to gene activation. Methylation at Lys-5 (H3K4me) facilitates subsequent acetylation of H3 and H4. Methylation at Lys-80 (H3K79me) is associated with DNA double-strand break (DSB) responses and is a specific target for TP53BP1. Methylation at Lys-10 (H3K9me) and Lys-28 (H3K27me) are linked to gene repression. Methylation at Lys-10 (H3K9me) is a specific target for HP1 proteins (CBX1, CBX3 and CBX5) and prevents subsequent phosphorylation at Ser-11 (H3S10ph) and acetylation of H3 and H4. Methylation at Lys-5 (H3K4me) and Lys-80 (H3K79me) require preliminary monoubiquitination of H2B at 'Lys-120'. Methylation at Lys-10 (H3K9me) and Lys-28 (H3K27me) are enriched in inactive X chromosome chromatin. Monomethylation at Lys-57 (H3K56me1) by EHMT2/G9A in G1 phase promotes interaction with PCNA and is required for DNA replication (By similarity).By similarity
Phosphorylated at Thr-4 (H3T3ph) by GSG2/haspin during prophase and dephosphorylated during anaphase. Phosphorylation at Ser-11 (H3S10ph) by AURKB is crucial for chromosome condensation and cell-cycle progression during mitosis and meiosis. In addition phosphorylation at Ser-11 (H3S10ph) by RPS6KA4 and RPS6KA5 is important during interphase because it enables the transcription of genes following external stimulation, like mitogens, stress, growth factors or UV irradiation and result in the activation of genes, such as c-fos and c-jun. Phosphorylation at Ser-11 (H3S10ph), which is linked to gene activation, prevents methylation at Lys-10 (H3K9me) but facilitates acetylation of H3 and H4. Phosphorylation at Ser-11 (H3S10ph) by AURKB mediates the dissociation of HP1 proteins (CBX1, CBX3 and CBX5) from heterochromatin. Phosphorylation at Ser-11 (H3S10ph) is also an essential regulatory mechanism for neoplastic cell transformation. Phosphorylated at Ser-29 (H3S28ph) by MLTK isoform 1, RPS6KA5 or AURKB during mitosis or upon ultraviolet B irradiation. Phosphorylation at Thr-7 (H3T6ph) by PRKCB is a specific tag for epigenetic transcriptional activation that prevents demethylation of Lys-5 (H3K4me) by LSD1/KDM1A. At centromeres, specifically phosphorylated at Thr-12 (H3T11ph) from prophase to early anaphase, by DAPK3 and PKN1. Phosphorylation at Thr-12 (H3T11ph) by PKN1 is a specific tag for epigenetic transcriptional activation that promotes demethylation of Lys-10 (H3K9me) by KDM4C/JMJD2C. Phosphorylation at Thr-12 (H3T11ph) by chromatin-associated CHEK1 regulates the transcription of cell cycle regulatory genes by modulating acetylation of Lys-10 (H3K9ac). Phosphorylation at Tyr-42 (H3Y41ph) by JAK2 promotes exclusion of CBX5 (HP1 alpha) from chromatin (By similarity).By similarity
Ubiquitinated by the CUL4-DDB-RBX1 complex in response to ultraviolet irradiation. This may weaken the interaction between histones and DNA and facilitate DNA accessibility to repair proteins. Monoubiquitinated by RAG1 in lymphoid cells, monoubiquitination is required for V(D)J recombination (By similarity). Ubiquitinated in testes.By similarity1 Publication
Lysine deamination at Lys-5 (H3K4all) to form allysine is mediated by LOXL2. Allysine formation by LOXL2 only takes place on H3K4me3 and results in gene repression (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, Citrullination, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiQ6LED0.
PRIDEiQ6LED0.

PTM databases

iPTMnetiQ6LED0.
PhosphoSiteiQ6LED0.

Expressioni

Developmental stagei

Expressed during S phase, then expression strongly decreases as cell division slows down during the process of differentiation.

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

IntActiQ6LED0. 2 interactions.
STRINGi10116.ENSRNOP00000067217.

Structurei

3D structure databases

ProteinModelPortaliQ6LED0.
SMRiQ6LED0. Positions 17-136.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H3 family.Curated

Phylogenomic databases

eggNOGiKOG1745. Eukaryota.
COG2036. LUCA.
GeneTreeiENSGT00760000118967.
HOGENOMiHOG000155290.
HOVERGENiHBG001172.
InParanoidiQ6LED0.
KOiK11253.
OMAiLARRIRX.
OrthoDBiEOG7HB5C2.
PhylomeDBiQ6LED0.
TreeFamiTF314241.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_H2A/H2B/H3.
IPR000164. Histone_H3/CENP-A.
[Graphical view]
PANTHERiPTHR11426. PTHR11426. 1 hit.
PfamiPF00125. Histone. 1 hit.
[Graphical view]
PRINTSiPR00622. HISTONEH3.
SMARTiSM00428. H3. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00322. HISTONE_H3_1. 1 hit.
PS00959. HISTONE_H3_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q6LED0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR
60 70 80 90 100
EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSAV MALQEACEAY
110 120 130
LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA
Length:136
Mass (Da):15,404
Last modified:January 23, 2007 - v3
Checksum:i9B89008EA50A0EF6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L19706 Genomic DNA. Translation: AAA19824.1.
RefSeqiNP_001013074.1. NM_001013056.1.
UniGeneiRn.230771.

Genome annotation databases

EnsembliENSRNOT00000072019; ENSRNOP00000064431; ENSRNOG00000046144.
ENSRNOT00000073188; ENSRNOP00000067217; ENSRNOG00000046434.
ENSRNOT00000079880; ENSRNOP00000074909; ENSRNOG00000054539.
ENSRNOT00000083417; ENSRNOP00000069899; ENSRNOG00000056281.
GeneIDi291159.
KEGGirno:291159.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L19706 Genomic DNA. Translation: AAA19824.1.
RefSeqiNP_001013074.1. NM_001013056.1.
UniGeneiRn.230771.

3D structure databases

ProteinModelPortaliQ6LED0.
SMRiQ6LED0. Positions 17-136.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ6LED0. 2 interactions.
STRINGi10116.ENSRNOP00000067217.

PTM databases

iPTMnetiQ6LED0.
PhosphoSiteiQ6LED0.

Proteomic databases

PaxDbiQ6LED0.
PRIDEiQ6LED0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000072019; ENSRNOP00000064431; ENSRNOG00000046144.
ENSRNOT00000073188; ENSRNOP00000067217; ENSRNOG00000046434.
ENSRNOT00000079880; ENSRNOP00000074909; ENSRNOG00000054539.
ENSRNOT00000083417; ENSRNOP00000069899; ENSRNOG00000056281.
GeneIDi291159.
KEGGirno:291159.

Organism-specific databases

CTDi291159.

Phylogenomic databases

eggNOGiKOG1745. Eukaryota.
COG2036. LUCA.
GeneTreeiENSGT00760000118967.
HOGENOMiHOG000155290.
HOVERGENiHBG001172.
InParanoidiQ6LED0.
KOiK11253.
OMAiLARRIRX.
OrthoDBiEOG7HB5C2.
PhylomeDBiQ6LED0.
TreeFamiTF314241.

Enzyme and pathway databases

ReactomeiR-RNO-212300. PRC2 methylates histones and DNA.
R-RNO-2559580. Oxidative Stress Induced Senescence.
R-RNO-2559582. Senescence-Associated Secretory Phenotype (SASP).
R-RNO-3214841. PKMTs methylate histone lysines.
R-RNO-3214842. HDMs demethylate histones.
R-RNO-3214847. HATs acetylate histones.
R-RNO-3214858. RMTs methylate histone arginines.
R-RNO-3247509. Chromatin modifying enzymes.
R-RNO-427359. SIRT1 negatively regulates rRNA Expression.
R-RNO-427413. NoRC negatively regulates rRNA expression.
R-RNO-5250924. B-WICH complex positively regulates rRNA expression.
R-RNO-5578749. Transcriptional regulation by small RNAs.
R-RNO-5625886. Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3.
R-RNO-73728. RNA Polymerase I Promoter Opening.
R-RNO-73777. RNA Polymerase I Chain Elongation.
R-RNO-983231. Factors involved in megakaryocyte development and platelet production.

Miscellaneous databases

NextBioi632205.
PROiQ6LED0.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_H2A/H2B/H3.
IPR000164. Histone_H3/CENP-A.
[Graphical view]
PANTHERiPTHR11426. PTHR11426. 1 hit.
PfamiPF00125. Histone. 1 hit.
[Graphical view]
PRINTSiPR00622. HISTONEH3.
SMARTiSM00428. H3. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00322. HISTONE_H3_1. 1 hit.
PS00959. HISTONE_H3_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "A B2-L1 composite between rat histone H2A and H3 genes."
    Choi Y.C., Han B.D., Chae C.-B.
    Mamm. Genome 5:52-54(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: Sprague-Dawley.
    Tissue: Liver.
  2. Lubec G., Kang S.U., Lubec S.
    Submitted (SEP-2007) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 58-64, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: Sprague-Dawley.
    Tissue: Brain.
  3. "Ubiquitination of histone H3 in elongating spermatids of rat testes."
    Chen H.Y., Sun J.-M., Zhang Y., Davie J.R., Meistrich M.L.
    J. Biol. Chem. 273:13165-13169(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION.
  4. "Novel mitosis-specific phosphorylation of histone H3 at Thr11 mediated by Dlk/ZIP kinase."
    Preuss U., Landsberg G., Scheidtmann K.H.
    Nucleic Acids Res. 31:878-885(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION AT SER-11 AND THR-12.

Entry informationi

Entry nameiH31_RAT
AccessioniPrimary (citable) accession number: Q6LED0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 17, 2006
Last sequence update: January 23, 2007
Last modified: May 11, 2016
This is version 108 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Miscellaneous

This histone is only present in mammals.

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. 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.