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Q6PI20

- H33_DANRE

UniProt

Q6PI20 - H33_DANRE

Protein

Histone H3.3

Gene

h3f3a

more
Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript leveli
  1. Functioni

    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.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei32 – 321Interaction with zmynd11By similarity

    GO - Molecular functioni

    1. DNA binding Source: UniProtKB-KW

    GO - Biological processi

    1. nucleosome assembly Source: InterPro

    Keywords - Ligandi

    DNA-binding

    Enzyme and pathway databases

    ReactomeiREACT_207282. PRC2 methylates histones and DNA.
    REACT_222268. Factors involved in megakaryocyte development and platelet production.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Histone H3.3
    Gene namesi
    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
    OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
    Taxonomic identifieri7955 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
    ProteomesiUP000000437: Chromosome 3, UP000000437: Chromosome 5

    Subcellular locationi

    GO - Cellular componenti

    1. nucleosome Source: UniProtKB-KW
    2. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Chromosome, Nucleosome core, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11RemovedBy similarity
    Chaini2 – 136135Histone H3.3PRO_0000253956Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei3 – 31Asymmetric dimethylarginine; by PRMT6By 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-methyllysine; alternateBy similarity
    Modified residuei7 – 71Phosphothreonine; by PKCBy similarity
    Modified residuei10 – 101N6-methylated lysineBy similarity
    Modified residuei11 – 111Phosphoserine; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5By similarity
    Modified residuei12 – 121Phosphothreonine; by PKCBy similarity
    Modified residuei15 – 151N6-acetyllysineBy similarity
    Modified residuei18 – 181Asymmetric dimethylarginineBy similarity
    Modified residuei19 – 191N6-acetyllysine; alternateBy similarity
    Modified residuei19 – 191N6-methylated lysine; alternateBy similarity
    Modified residuei24 – 241N6-acetyllysineBy similarity
    Modified residuei28 – 281N6-acetyllysine; alternateBy similarity
    Modified residuei28 – 281N6-methylated lysine; alternateBy similarity
    Modified residuei29 – 291Phosphoserine; by AURKB, AURKC and RPS6KA5By similarity
    Modified residuei37 – 371N6-acetyllysine; alternateBy similarity
    Modified residuei37 – 371N6-methylated lysine; alternateBy similarity
    Modified residuei42 – 421PhosphotyrosineBy similarity
    Modified residuei58 – 581PhosphoserineBy similarity
    Modified residuei65 – 651N6-methylated lysineBy similarity
    Modified residuei80 – 801N6-methylated lysineBy similarity
    Modified residuei81 – 811PhosphothreonineBy 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-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
    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.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.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.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

    Keywords - PTMi

    Acetylation, Methylation, Phosphoprotein, Ubl conjugation

    Proteomic databases

    PRIDEiQ6PI20.

    Expressioni

    Developmental stagei

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

    Gene expression databases

    BgeeiQ6PI20.

    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. Interacts with zmynd11; when trimethylated at 'Lys-36' (H3.3K36me3).

    Protein-protein interaction databases

    BioGridi95374. 1 interaction.
    STRINGi7955.ENSDARP00000101697.

    Structurei

    3D structure databases

    ProteinModelPortaliQ6PI20.
    SMRiQ6PI20. Positions 17-136.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domaini

    Specific interaction of trimethylated form at 'Lys-36' (H3.3K36me3) with zmynd11 is mediated by the encapsulation of Ser-32 residue with a composite pocket formed by the tandem bromo-PWWP domains.By similarity

    Sequence similaritiesi

    Belongs to the histone H3 family.Curated

    Phylogenomic databases

    eggNOGiCOG2036.
    GeneTreeiENSGT00750000117538.
    HOGENOMiHOG000155290.
    HOVERGENiHBG001172.
    InParanoidiQ6PI20.
    KOiK11253.
    OMAiHIVMART.
    OrthoDBiEOG7HB5C2.
    PhylomeDBiQ6PI20.
    TreeFamiTF314241.

    Family and domain databases

    Gene3Di1.10.20.10. 1 hit.
    InterProiIPR009072. Histone-fold.
    IPR007125. Histone_core_D.
    IPR000164. Histone_H3.
    [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.

    Q6PI20-1 [UniParc]FASTAAdd to Basket

    « Hide

    MARTKQTARK STGGKAPRKQ LATKAARKSA PSTGGVKKPH RYRPGTVALR    50
    EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSAAI GALQEASEAY 100
    LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA 136
    Length:136
    Mass (Da):15,328
    Last modified:January 23, 2007 - v3
    Checksum:i5158ED279E6F9E1C
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti50 – 501R → G in AAH45982. 1 PublicationCurated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    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.
    RefSeqiNP_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.
    UniGeneiDr.42924.
    Dr.75577.
    Dr.75603.
    Dr.77073.

    Genome annotation databases

    EnsembliENSDART00000027623; ENSDARP00000006849; ENSDARG00000020504.
    ENSDART00000047269; ENSDARP00000047268; ENSDARG00000033009.
    ENSDART00000066545; ENSDARP00000066544; ENSDARG00000045248.
    ENSDART00000098982; ENSDARP00000089753; ENSDARG00000068436.
    ENSDART00000137017; ENSDARP00000117879; ENSDARG00000045248.
    ENSDART00000146211; ENSDARP00000120344; ENSDARG00000020504.
    ENSDART00000151594; ENSDARP00000125972; ENSDARG00000068436.
    ENSDART00000151600; ENSDARP00000126130; ENSDARG00000068434.
    GeneIDi100331798.
    336231.
    394076.
    406269.
    550262.
    KEGGidre:100331798.
    dre:336231.
    dre:394076.
    dre:406269.
    dre:550262.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    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 .
    RefSeqi NP_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.
    UniGenei Dr.42924.
    Dr.75577.
    Dr.75603.
    Dr.77073.

    3D structure databases

    ProteinModelPortali Q6PI20.
    SMRi Q6PI20. Positions 17-136.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 95374. 1 interaction.
    STRINGi 7955.ENSDARP00000101697.

    Proteomic databases

    PRIDEi Q6PI20.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSDART00000027623 ; ENSDARP00000006849 ; ENSDARG00000020504 .
    ENSDART00000047269 ; ENSDARP00000047268 ; ENSDARG00000033009 .
    ENSDART00000066545 ; ENSDARP00000066544 ; ENSDARG00000045248 .
    ENSDART00000098982 ; ENSDARP00000089753 ; ENSDARG00000068436 .
    ENSDART00000137017 ; ENSDARP00000117879 ; ENSDARG00000045248 .
    ENSDART00000146211 ; ENSDARP00000120344 ; ENSDARG00000020504 .
    ENSDART00000151594 ; ENSDARP00000125972 ; ENSDARG00000068436 .
    ENSDART00000151600 ; ENSDARP00000126130 ; ENSDARG00000068434 .
    GeneIDi 100331798.
    336231.
    394076.
    406269.
    550262.
    KEGGi dre:100331798.
    dre:336231.
    dre:394076.
    dre:406269.
    dre:550262.

    Organism-specific databases

    CTDi 3020.
    394076.
    440093.
    550262.

    Phylogenomic databases

    eggNOGi COG2036.
    GeneTreei ENSGT00750000117538.
    HOGENOMi HOG000155290.
    HOVERGENi HBG001172.
    InParanoidi Q6PI20.
    KOi K11253.
    OMAi HIVMART.
    OrthoDBi EOG7HB5C2.
    PhylomeDBi Q6PI20.
    TreeFami TF314241.

    Enzyme and pathway databases

    Reactomei REACT_207282. PRC2 methylates histones and DNA.
    REACT_222268. Factors involved in megakaryocyte development and platelet production.

    Miscellaneous databases

    NextBioi 20811638.
    PROi Q6PI20.

    Gene expression databases

    Bgeei Q6PI20.

    Family and domain databases

    Gene3Di 1.10.20.10. 1 hit.
    InterProi IPR009072. Histone-fold.
    IPR007125. Histone_core_D.
    IPR000164. Histone_H3.
    [Graphical view ]
    PANTHERi PTHR11426. PTHR11426. 1 hit.
    Pfami PF00125. Histone. 1 hit.
    [Graphical view ]
    PRINTSi PR00622. HISTONEH3.
    SMARTi SM00428. H3. 1 hit.
    [Graphical view ]
    SUPFAMi SSF47113. SSF47113. 1 hit.
    PROSITEi PS00322. HISTONE_H3_1. 1 hit.
    PS00959. HISTONE_H3_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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.

    Entry informationi

    Entry nameiH33_DANRE
    AccessioniPrimary (citable) accession number: Q6PI20
    Secondary accession number(s): A5PL96, Q7ZV67
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 17, 2006
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    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

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3