Histone H3.3 - Rattus norvegicus (Rat)

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P84245 (H33_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 83. History...

Clusters with 100%, 90%, 50% identity |

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Histone H3.3

Gene names

Name:	H3f3b
Synonyms:	H3.3b

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

Protein attributes

Sequence length	136 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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.
Subunit structure	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.
Subcellular location	Nucleus By similarity. Chromosome By similarity.
Developmental stage	Expressed throughout the cell cycle independently of DNA synthesis. Levels increase from embryonic day 18 to postnatal day 10. Ref.1
Post-translational modification	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) 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.
Sequence similarities	Belongs to the histone H3 family.

Ontologies

Keywords
Cellular component	Chromosome Nucleosome core Nucleus
Ligand	DNA-binding
PTM	Acetylation Citrullination Methylation Phosphoprotein Ubl conjugation
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	brain development Inferred from expression pattern Ref.1. Source: RGD nucleosome assembly Inferred from electronic annotation. Source: InterPro response to hormone stimulus Inferred from expression pattern PubMed 8587656. Source: RGD
Cellular_component	nucleosome Inferred from electronic annotation. Source: UniProtKB-KW nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed By similarity

Chain

2 – 136

135

Histone H3.3

PRO_0000221254

Amino acid modifications

Modified residue

Asymmetric dimethylarginine; by PRMT6 By similarity

Modified residue

Phosphothreonine; by GSG2 By similarity

Modified residue

Allysine; alternate By similarity

Modified residue

N6,N6,N6-trimethyllysine; alternate By similarity

Modified residue

N6,N6-dimethyllysine; alternate By similarity

Modified residue

N6-acetyllysine; alternate By similarity

Modified residue

N6-crotonyl-L-lysine; alternate By similarity

Modified residue

N6-methyllysine; alternate By similarity

Modified residue

Phosphothreonine; by PKC By similarity

Modified residue

Citrulline; alternate By similarity

Modified residue

Symmetric dimethylarginine; by PRMT5; alternate By similarity

Modified residue

N6,N6,N6-trimethyllysine; alternate By similarity

Modified residue

N6,N6-dimethyllysine; alternate By similarity

Modified residue

N6-acetyllysine; alternate By similarity

Modified residue

N6-crotonyl-L-lysine; alternate By similarity

Modified residue

N6-methyllysine; alternate By similarity

Modified residue

Phosphoserine; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5 Ref.3

Modified residue

Phosphothreonine; by PKC Ref.3

Modified residue

N6-acetyllysine By similarity

Modified residue

Asymmetric dimethylarginine; by CARM1; alternate By similarity

Modified residue

Citrulline; alternate By similarity

Modified residue

N6-acetyllysine; alternate By similarity

Modified residue

N6-crotonyl-L-lysine; alternate By similarity

Modified residue

N6-methyllysine; alternate By similarity

Modified residue

N6-acetyllysine; alternate By similarity

Modified residue

N6-crotonyl-L-lysine; alternate By similarity

Modified residue

N6-methyllysine; alternate By similarity

Modified residue

N6,N6,N6-trimethyllysine; alternate By similarity

Modified residue

N6,N6-dimethyllysine; alternate By similarity

Modified residue

N6-acetyllysine; alternate By similarity

Modified residue

N6-crotonyl-L-lysine; alternate By similarity

Modified residue

N6-methylated lysine; alternate By similarity

Modified residue

N6-methyllysine; alternate By similarity

Modified residue

Phosphoserine; by AURKB, AURKC and RPS6KA5 By similarity

Modified residue

Phosphoserine By similarity

Modified residue

N6,N6,N6-trimethyllysine; alternate By similarity

Modified residue

N6,N6-dimethyllysine; alternate By similarity

Modified residue

N6-acetyllysine; alternate Ref.5

Modified residue

N6-methyllysine; alternate By similarity

Modified residue

N6-methyllysine By similarity

Modified residue

Phosphotyrosine By similarity

Modified residue

N6,N6,N6-trimethyllysine; alternate By similarity

Modified residue

N6-acetyllysine; alternate By similarity

Modified residue

N6-crotonyl-L-lysine; alternate By similarity

Modified residue

N6-methyllysine; by EHMT2; alternate By similarity

Modified residue

Phosphoserine By similarity

Modified residue

N6-methyllysine By similarity

Modified residue

N6,N6,N6-trimethyllysine; alternate By similarity

Modified residue

N6,N6-dimethyllysine; alternate By similarity

Modified residue

N6-acetyllysine; alternate By similarity

Modified residue

N6-methyllysine; alternate By similarity

Modified residue

Phosphothreonine By similarity

Modified residue

123

N6-acetyllysine By similarity

Modified residue

123

N6-methyllysine; alternate By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

P84245 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 5158ED279E6F9E1C
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FASTA

136

15,328

        10         20         30         40         50         60 
MARTKQTARK STGGKAPRKQ LATKAARKSA PSTGGVKKPH RYRPGTVALR EIRRYQKSTE 

        70         80         90        100        110        120 
LLIRKLPFQR LVREIAQDFK TDLRFQSAAI GALQEASEAY LVGLFEDTNL CAIHAKRVTI 

       130 
MPKDIQLARR IRGERA

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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. Strain: Sprague-Dawley. Tissue: Embryonic brain.
[2]	"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.
[3]	"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.
[4]	"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.
[5]	"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.

Cross-references

Sequence databases
EMBL GenBank DDBJ	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.
IPI	IPI00231475.
PIR	S34185.
RefSeq	NP_446437.1. NM_053985.2. XP_002728089.1. XM_002728043.2. XP_003752732.1. XM_003752684.1.
UniGene	Rn.124815. Rn.198918. Rn.29857.
3D structure databases
ProteinModelPortal	P84245.
ModBase	Search...
Proteomic databases
PaxDb	P84245.
PRIDE	P84245.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENSRNOT00000004329; ENSRNOP00000004329; ENSRNOG00000003220. ENSRNOT00000050223; ENSRNOP00000040434; ENSRNOG00000006532.
GeneID	100361558. 117056.
KEGG	rno:100361558. rno:117056.
Organism-specific databases
CTD	3021.
RGD	621095. H3f3b.
Phylogenomic databases
eggNOG	COG2036.
GeneTree	ENSGT00670000097754.
HOGENOM	HOG000155290.
HOVERGEN	HBG001172.
InParanoid	P84245.
KO	K11253.
OMA	CCIRGER.
OrthoDB	EOG4V9TS1.
Gene expression databases
ArrayExpress	P84245.
Genevestigator	P84245.
GermOnline	ENSRNOG00000003220. Rattus norvegicus.
Family and domain databases
Gene3D	1.10.20.10. 1 hit.
InterPro	IPR009072. Histone-fold. IPR007125. Histone_core_D. IPR000164. Histone_H3. [Graphical view]
PANTHER	PTHR11426. PTHR11426. 1 hit.
Pfam	PF00125. Histone. 1 hit. [Graphical view]
PRINTS	PR00622. HISTONEH3.
SMART	SM00428. H3. 1 hit. [Graphical view]
SUPFAM	SSF47113. Histone-fold. 1 hit.
PROSITE	PS00322. HISTONE_H3_1. 1 hit. PS00959. HISTONE_H3_2. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	619898.

Entry information

Entry name

H33_RAT

Accession

Primary (citable) accession number: P84245
Secondary accession number(s): P06351

Q9V3W4

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1988
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 83 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Amino acid modifications

Sequences

References

Cross-references

Sequence databases

3D structure databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents