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Q6PI20 (H33_DANRE) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 105. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Histone H3.3
Gene names
Name:h3f3a
ORF Names:zgc:56193, zgc:86731
AND
Name:h3f3b.1
ORF Names:zgc:110292
AND
Name:h3f3c
ORF Names:zgc:64222
AND
Name:h3f3d
ORF Names:zgc:56418
OrganismDanio rerio (Zebrafish) (Brachydanio rerio) [Reference proteome]
Taxonomic identifier7955 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio

Protein attributes

Sequence length136 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at transcript 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.

Subcellular location

Nucleus. Chromosome.

Developmental stage

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

Post-translational modification

Acetylation is generally linked to gene activation. 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.

Asymmetric dimethylation at Arg-18 (H3R17me2a) is linked to gene activation. 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 (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' 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.

Monoubiquitinated by rag1 in lymphoid cells, monoubiquitination is required for V(D)J recombination By similarity.

Lysine deamination at Lys-5 (H3K4all) to form allysine only takes place on H3K4me3 and results in gene repression By similarity.

Sequence similarities

Belongs to the histone H3 family.

Ontologies

Keywords
   Cellular componentChromosome
Nucleosome core
Nucleus
   LigandDNA-binding
   PTMAcetylation
Methylation
Phosphoprotein
Ubl conjugation
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processnucleosome assembly

Inferred from electronic annotation. Source: InterPro

   Cellular_componentnucleosome

Inferred from electronic annotation. Source: UniProtKB-KW

nucleus

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionDNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed By similarity
Chain2 – 136135Histone H3.3
PRO_0000253956

Amino acid modifications

Modified residue31Asymmetric dimethylarginine; by PRMT6 By similarity
Modified residue41Phosphothreonine; by GSG2 By similarity
Modified residue51Allysine; alternate By similarity
Modified residue51N6,N6,N6-trimethyllysine; alternate By similarity
Modified residue51N6,N6-dimethyllysine; alternate By similarity
Modified residue51N6-acetyllysine; alternate By similarity
Modified residue51N6-methyllysine; alternate By similarity
Modified residue71Phosphothreonine; by PKC By similarity
Modified residue101N6-methylated lysine By similarity
Modified residue111Phosphoserine; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5 By similarity
Modified residue121Phosphothreonine; by PKC By similarity
Modified residue151N6-acetyllysine By similarity
Modified residue181Asymmetric dimethylarginine By similarity
Modified residue191N6-acetyllysine; alternate By similarity
Modified residue191N6-methylated lysine; alternate By similarity
Modified residue241N6-acetyllysine By similarity
Modified residue281N6-acetyllysine; alternate By similarity
Modified residue281N6-methylated lysine; alternate By similarity
Modified residue291Phosphoserine; by AURKB, AURKC and RPS6KA5 By similarity
Modified residue371N6-acetyllysine; alternate By similarity
Modified residue371N6-methylated lysine; alternate By similarity
Modified residue421Phosphotyrosine By similarity
Modified residue581Phosphoserine By similarity
Modified residue651N6-methylated lysine By similarity
Modified residue801N6-methylated lysine By similarity
Modified residue811Phosphothreonine By similarity
Modified residue1161N6-acetyllysine By similarity
Modified residue1231N6-acetyllysine; alternate By similarity
Modified residue1231N6-methyllysine; alternate By similarity

Experimental info

Sequence conflict501R → G in AAH45982. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Q6PI20 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: 5158ED279E6F9E1C

FASTA13615,328
        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

[1]NIH - Zebrafish Gene Collection (ZGC) project
Submitted (OCT-2007) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Strain: SJD and WIK.
Tissue: Embryo and Olfactory epithelium.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
BC045982 mRNA. Translation: AAH45982.1.
BC049017 mRNA. Translation: AAH49017.1.
BC057444 mRNA. Translation: AAH57444.1.
BC071406 mRNA. Translation: AAH71406.1.
BC092854 mRNA. Translation: AAH92854.1.
BC152134 mRNA. Translation: AAI52135.1.
BC154269 mRNA. Translation: AAI54270.1.
RefSeqNP_001017599.1. NM_001017599.1.
NP_956297.1. NM_200003.1.
NP_957395.1. NM_201101.1.
NP_998161.1. NM_212996.1.
XP_002664801.1. XM_002664755.3.
XP_005164281.1. XM_005164224.1.
UniGeneDr.42924.
Dr.75577.
Dr.75603.
Dr.77073.

3D structure databases

ProteinModelPortalQ6PI20.
SMRQ6PI20. Positions 17-136.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid95374. 1 interaction.
STRING7955.ENSDARP00000101697.

Proteomic databases

PRIDEQ6PI20.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSDART00000027623; ENSDARP00000006849; ENSDARG00000020504.
ENSDART00000047269; ENSDARP00000047268; ENSDARG00000033009.
ENSDART00000066545; ENSDARP00000066544; ENSDARG00000045248.
ENSDART00000098982; ENSDARP00000089753; ENSDARG00000068436.
ENSDART00000137017; ENSDARP00000117879; ENSDARG00000045248.
ENSDART00000146211; ENSDARP00000120344; ENSDARG00000020504.
ENSDART00000151594; ENSDARP00000125972; ENSDARG00000068436.
ENSDART00000151600; ENSDARP00000126130; ENSDARG00000068434.
GeneID100331798.
336231.
394076.
406269.
550262.
KEGGdre:100331798.
dre:336231.
dre:394076.
dre:406269.
dre:550262.

Organism-specific databases

CTD3020.
394076.
440093.
550262.

Phylogenomic databases

eggNOGCOG2036.
GeneTreeENSGT00750000117538.
HOGENOMHOG000155290.
HOVERGENHBG001172.
InParanoidQ6PI20.
KOK11253.
OMAQEATESY.
OrthoDBEOG7HB5C2.
PhylomeDBQ6PI20.
TreeFamTF314241.

Gene expression databases

BgeeQ6PI20.

Family and domain databases

Gene3D1.10.20.10. 1 hit.
InterProIPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR000164. Histone_H3.
[Graphical view]
PANTHERPTHR11426. PTHR11426. 1 hit.
PfamPF00125. Histone. 1 hit.
[Graphical view]
PRINTSPR00622. HISTONEH3.
SMARTSM00428. H3. 1 hit.
[Graphical view]
SUPFAMSSF47113. SSF47113. 1 hit.
PROSITEPS00322. HISTONE_H3_1. 1 hit.
PS00959. HISTONE_H3_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio20811638.
PROQ6PI20.

Entry information

Entry nameH33_DANRE
AccessionPrimary (citable) accession number: Q6PI20
Secondary accession number(s): A5PL96, Q7ZV67
Entry history
Integrated into UniProtKB/Swiss-Prot: October 17, 2006
Last sequence update: January 23, 2007
Last modified: April 16, 2014
This is version 105 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families