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Q6PI79

- H33_XENLA

UniProt

Q6PI79 - H33_XENLA

Protein

Histone H3.3

Gene
N/A
Organism
Xenopus laevis (African clawed frog)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein 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

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Histone H3.3
    OrganismiXenopus laevis (African clawed frog)
    Taxonomic identifieri8355 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

    Organism-specific databases

    XenbaseiXB-GENE-488762. h3f3b.

    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_0000253957Add
    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; alternate1 Publication
    Modified residuei5 – 51N6,N6-dimethyllysine; alternate1 Publication
    Modified residuei5 – 51N6-acetyllysine; alternateBy similarity
    Modified residuei5 – 51N6-methyllysine; alternate1 Publication
    Modified residuei7 – 71Phosphothreonine; by PKCBy similarity
    Modified residuei10 – 101N6-methylated lysine1 Publication
    Modified residuei11 – 111Phosphoserine; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5By similarity
    Modified residuei12 – 121Phosphothreonine; by PKCBy similarity
    Modified residuei15 – 151N6-acetyllysine1 Publication
    Modified residuei18 – 181Asymmetric dimethylarginine1 Publication
    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.1 Publication
    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

    PRIDEiQ6PI79.

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

    Structurei

    3D structure databases

    ProteinModelPortaliQ6PI79.
    SMRiQ6PI79. 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

    HOVERGENiHBG001172.
    KOiK11253.

    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.

    Q6PI79-1 [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

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BC041218 mRNA. Translation: AAH41218.1.
    BC042290 mRNA. Translation: AAH42290.1.
    BC042309 mRNA. Translation: AAH42309.1.
    BC070966 mRNA. Translation: AAH70966.1.
    BC074158 mRNA. Translation: AAH74158.1.
    BC106302 mRNA. Translation: AAI06303.1.
    BC123120 mRNA. Translation: AAI23121.1.
    RefSeqiNP_001079375.1. NM_001085906.1.
    NP_001080065.1. NM_001086596.1.
    NP_001085048.1. NM_001091579.1.
    NP_001086074.1. NM_001092605.1.
    NP_001091902.1. NM_001098432.1.
    UniGeneiXl.36404.
    Xl.39769.
    Xl.4043.
    Xl.77438.
    Xl.86817.

    Genome annotation databases

    GeneIDi379062.
    379757.
    399418.
    432115.
    444503.
    KEGGixla:379062.
    xla:379757.
    xla:399418.
    xla:432115.
    xla:444503.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BC041218 mRNA. Translation: AAH41218.1 .
    BC042290 mRNA. Translation: AAH42290.1 .
    BC042309 mRNA. Translation: AAH42309.1 .
    BC070966 mRNA. Translation: AAH70966.1 .
    BC074158 mRNA. Translation: AAH74158.1 .
    BC106302 mRNA. Translation: AAI06303.1 .
    BC123120 mRNA. Translation: AAI23121.1 .
    RefSeqi NP_001079375.1. NM_001085906.1.
    NP_001080065.1. NM_001086596.1.
    NP_001085048.1. NM_001091579.1.
    NP_001086074.1. NM_001092605.1.
    NP_001091902.1. NM_001098432.1.
    UniGenei Xl.36404.
    Xl.39769.
    Xl.4043.
    Xl.77438.
    Xl.86817.

    3D structure databases

    ProteinModelPortali Q6PI79.
    SMRi Q6PI79. Positions 17-136.
    ModBasei Search...
    MobiDBi Search...

    Proteomic databases

    PRIDEi Q6PI79.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 379062.
    379757.
    399418.
    432115.
    444503.
    KEGGi xla:379062.
    xla:379757.
    xla:399418.
    xla:432115.
    xla:444503.

    Organism-specific databases

    CTDi 3020.
    3021.
    653604.
    Xenbasei XB-GENE-488762. h3f3b.

    Phylogenomic databases

    HOVERGENi HBG001172.
    KOi K11253.

    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 - Xenopus Gene Collection (XGC) project
      Submitted (SEP-2006) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Embryo.
    2. "Involvement of histone methylation and phosphorylation in regulation of transcription by thyroid hormone receptor."
      Li J., Lin Q., Yoon H.-G., Huang Z.-Q., Strahl B.D., Allis C.D., Wong J.
      Mol. Cell. Biol. 22:5688-5697(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: METHYLATION AT LYS-5; LYS-10 AND ARG-18, PHOSPHORYLATION AT SER-11, ACETYLATION AT LYS-15.

    Entry informationi

    Entry nameiH33_XENLA
    AccessioniPrimary (citable) accession number: Q6PI79
    Secondary accession number(s): Q05AX9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 17, 2006
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 79 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3