P84245 (H33_RAT) Reviewed, UniProtKB/Swiss-Prot
Last modified November 13, 2013. Version 86. History...
Names and origin
|Protein names||Recommended name:|
|Organism||Rattus norvegicus (Rat) [Reference proteome]|
|Taxonomic identifier||10116 [NCBI]|
|Taxonomic lineage||Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Rattus|
|Sequence length||136 AA.|
|Sequence processing||The displayed sequence is further processed into a mature form.|
|Protein existence||Evidence at protein level|
General annotation (Comments)
Variant histone H3 which replaces conventional H3 in a wide range of nucleosomes in active genes. Constitutes the predominant form of histone H3 in non-dividing cells and is incorporated into chromatin independently of DNA synthesis. Deposited at sites of nucleosomal displacement throughout transcribed genes, suggesting that it represents an epigenetic imprint of transcriptionally active chromatin. 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.
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. Interacts with HIRA, a chaperone required for its incorporation into nucleosomes.
Expressed throughout the cell cycle independently of DNA synthesis. Levels increase from embryonic day 18 to postnatal day 10. Ref.1
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.
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.
Specifically enriched in modifications associated with active chromatin such as methylation at Lys-5 (H3K4me), Lys-37 and Lys-80. 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), which are linked to gene repression, are underrepresented. 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.
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 Tyr-42 (H3Y41ph) by JAK2 promotes exclusion of CBX5 (HP1 alpha) from chromatin. Phosphorylation on Ser-32 (H3S31ph) is specific to regions bordering centromeres in metaphase chromosomes By similarity. Ref.3
Monoubiquitinated by RAG1 in lymphoid cells, monoubiquitination is required for V(D)J recombination By similarity. Ubiquitinated in testes. Ref.4
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.
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.
Belongs to the histone H3 family.
|Technical term||Complete proteome|
|Gene Ontology (GO)|
|Biological_process||brain developmentnucleosome assembly|
Inferred from electronic annotation. Source: InterProresponse to hormone stimulus
Inferred from electronic annotation. Source: UniProtKB-KWnucleus
Inferred from electronic annotation. Source: UniProtKB-SubCell
Inferred from electronic annotation. Source: UniProtKB-KW
|Complete GO annotation...|
Sequence annotation (Features)
|Feature key||Position(s)||Length||Description||Graphical view||Feature identifier|
|Initiator methionine||1||1||Removed By similarity|
|Chain||2 – 136||135||Histone H3.3||PRO_0000221254|
Amino acid modifications
|Modified residue||3||1||Asymmetric dimethylarginine; by PRMT6 By similarity|
|Modified residue||4||1||Phosphothreonine; by GSG2 By similarity|
|Modified residue||5||1||Allysine; alternate By similarity|
|Modified residue||5||1||N6,N6,N6-trimethyllysine; alternate By similarity|
|Modified residue||5||1||N6,N6-dimethyllysine; alternate By similarity|
|Modified residue||5||1||N6-acetyllysine; alternate By similarity|
|Modified residue||5||1||N6-crotonyl-L-lysine; alternate By similarity|
|Modified residue||5||1||N6-methyllysine; alternate By similarity|
|Modified residue||7||1||Phosphothreonine; by PKC By similarity|
|Modified residue||9||1||Citrulline; alternate By similarity|
|Modified residue||9||1||Symmetric dimethylarginine; by PRMT5; alternate By similarity|
|Modified residue||10||1||N6,N6,N6-trimethyllysine; alternate By similarity|
|Modified residue||10||1||N6,N6-dimethyllysine; alternate By similarity|
|Modified residue||10||1||N6-acetyllysine; alternate By similarity|
|Modified residue||10||1||N6-crotonyl-L-lysine; alternate By similarity|
|Modified residue||10||1||N6-methyllysine; alternate By similarity|
|Modified residue||11||1||Phosphoserine; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5 Ref.3|
|Modified residue||12||1||Phosphothreonine; by PKC Ref.3|
|Modified residue||15||1||N6-acetyllysine By similarity|
|Modified residue||18||1||Asymmetric dimethylarginine; by CARM1; alternate By similarity|
|Modified residue||18||1||Citrulline; alternate By similarity|
|Modified residue||19||1||N6-acetyllysine; alternate By similarity|
|Modified residue||19||1||N6-crotonyl-L-lysine; alternate By similarity|
|Modified residue||19||1||N6-methyllysine; alternate By similarity|
|Modified residue||24||1||N6-acetyllysine; alternate By similarity|
|Modified residue||24||1||N6-crotonyl-L-lysine; alternate By similarity|
|Modified residue||24||1||N6-methyllysine; alternate By similarity|
|Modified residue||28||1||N6,N6,N6-trimethyllysine; alternate By similarity|
|Modified residue||28||1||N6,N6-dimethyllysine; alternate By similarity|
|Modified residue||28||1||N6-acetyllysine; alternate By similarity|
|Modified residue||28||1||N6-crotonyl-L-lysine; alternate By similarity|
|Modified residue||28||1||N6-methyllysine; alternate By similarity|
|Modified residue||29||1||Phosphoserine; by AURKB, AURKC and RPS6KA5 By similarity|
|Modified residue||32||1||Phosphoserine By similarity|
|Modified residue||37||1||N6,N6,N6-trimethyllysine; alternate By similarity|
|Modified residue||37||1||N6,N6-dimethyllysine; alternate By similarity|
|Modified residue||37||1||N6-acetyllysine; alternate Ref.5|
|Modified residue||37||1||N6-methyllysine; alternate By similarity|
|Modified residue||38||1||N6-methyllysine By similarity|
|Modified residue||42||1||Phosphotyrosine By similarity|
|Modified residue||57||1||N6,N6,N6-trimethyllysine; alternate By similarity|
|Modified residue||57||1||N6-acetyllysine; alternate By similarity|
|Modified residue||57||1||N6-crotonyl-L-lysine; alternate By similarity|
|Modified residue||57||1||N6-methyllysine; by EHMT2; alternate By similarity|
|Modified residue||58||1||Phosphoserine By similarity|
|Modified residue||65||1||N6-methyllysine By similarity|
|Modified residue||80||1||N6,N6,N6-trimethyllysine; alternate By similarity|
|Modified residue||80||1||N6,N6-dimethyllysine; alternate By similarity|
|Modified residue||80||1||N6-acetyllysine; alternate By similarity|
|Modified residue||80||1||N6-methyllysine; alternate By similarity|
|Modified residue||81||1||Phosphothreonine By similarity|
|Modified residue||108||1||Phosphothreonine By similarity|
|Modified residue||116||1||N6-acetyllysine By similarity|
|Modified residue||123||1||N6-acetyllysine; alternate By similarity|
|Modified residue||123||1||N6-methyllysine; alternate By similarity|
|||"H1(0) and H3.3B mRNA levels in developing rat brain."|
Castiglia D., Cestelli A., Scaturro M., Nastasi T., Di Liegro I.
Neurochem. Res. 19:1531-1537(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], DEVELOPMENTAL STAGE.
Tissue: Embryonic brain.
|||"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].
Tissue: Brain, Pituitary and Testis.
|||"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.
|||"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.
|||"Mass spectrometry-compatible silver staining of histones resolved on acetic acid-urea-Triton PAGE."|
Pramod K.S., Bharat K., Sanjay G.
Proteomics 9:2589-2592(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY, ACETYLATION AT LYS-37.
|+||Additional computationally mapped references.|
|X73683 mRNA. Translation: CAA52035.1.|
BC063159 mRNA. Translation: AAH63159.1.
BC078759 mRNA. Translation: AAH78759.1.
BC086580 mRNA. Translation: AAH86580.1.
BC087725 mRNA. Translation: AAH87725.1.
|RefSeq||NP_446437.1. NM_053985.2. |
3D structure databases
|SMR||P84245. Positions 17-136. |
Protein-protein interaction databases
|IntAct||P84245. 1 interaction.|
Protocols and materials databases
Genome annotation databases
|Ensembl||ENSRNOT00000004329; ENSRNOP00000004329; ENSRNOG00000003220. |
ENSRNOT00000050223; ENSRNOP00000040434; ENSRNOG00000006532.
|RGD||621095. H3f3b. |
Gene expression databases
Family and domain databases
|Gene3D||22.214.171.124. 1 hit. |
|InterPro||IPR009072. Histone-fold. |
|PANTHER||PTHR11426. PTHR11426. 1 hit. |
|Pfam||PF00125. Histone. 1 hit. |
|PRINTS||PR00622. HISTONEH3. |
|SMART||SM00428. H3. 1 hit. |
|SUPFAM||SSF47113. SSF47113. 1 hit. |
|PROSITE||PS00322. HISTONE_H3_1. 1 hit. |
PS00959. HISTONE_H3_2. 1 hit.
|Accession||Primary (citable) accession number: P84245|
Secondary accession number(s): P06351 Q9V3W4
|Entry status||Reviewed (UniProtKB/Swiss-Prot)|
|Annotation program||Chordata Protein Annotation Program|
Index of protein domains and families