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P84233

- H32_XENLA

UniProt

P84233 - H32_XENLA

Protein

Histone H3.2

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

    Core component of nucleosome. 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.

    GO - Molecular functioni

    1. DNA binding Source: UniProtKB-KW
    2. protein binding Source: IntAct

    GO - Biological processi

    1. nucleosome assembly Source: InterPro

    Keywords - Ligandi

    DNA-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Histone H3.2
    OrganismiXenopus laevis (African clawed frog)
    Taxonomic identifieri8355 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

    Organism-specific databases

    XenbaseiXB-GENE-866635. hist2h3c.

    Subcellular locationi

    GO - Cellular componenti

    1. nucleoplasm Source: Reactome
    2. nucleosome Source: UniProtKB-KW

    Keywords - Cellular componenti

    Chromosome, Nucleosome core, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11RemovedBy similarity
    Chaini2 – 136135Histone H3.2PRO_0000221265Add
    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 By similarity.By similarity
    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 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

    PRIDEiP84233.

    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.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    P627992EBI-350041,EBI-302085

    Protein-protein interaction databases

    BioGridi674575. 2 interactions.
    DIPiDIP-37430N.
    IntActiP84233. 4 interactions.

    Structurei

    Secondary structure

    1
    136
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi7 – 104
    Beta strandi19 – 213
    Beta strandi27 – 293
    Beta strandi31 – 344
    Helixi46 – 5712
    Helixi65 – 7713
    Beta strandi80 – 823
    Helixi87 – 11428
    Beta strandi118 – 1203
    Helixi122 – 13110
    Turni132 – 1354

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1F66X-ray2.60A/E1-136[»]
    1KX3X-ray2.00A/E2-136[»]
    1KX4X-ray2.60A/E2-136[»]
    1KX5X-ray1.94A/E2-136[»]
    1P34X-ray2.70A/E2-136[»]
    1P3AX-ray3.00A/E2-136[»]
    1P3BX-ray3.00A/E2-136[»]
    1P3FX-ray2.90A/E2-136[»]
    1P3GX-ray2.70A/E2-136[»]
    1P3IX-ray2.30A/E2-136[»]
    1P3KX-ray2.90A/E2-136[»]
    1P3LX-ray2.40A/E2-136[»]
    1P3MX-ray2.90A/E2-136[»]
    1P3OX-ray2.75A/E2-136[»]
    1P3PX-ray2.70A/E2-136[»]
    1S32X-ray2.05A/E2-136[»]
    1ZBBX-ray9.00A/E/a/e2-136[»]
    1ZLAX-ray2.90A/E2-136[»]
    2F8NX-ray2.90A/E1-136[»]
    2FJ7X-ray3.20A/E2-136[»]
    2HUEX-ray1.70B62-136[»]
    2IO5X-ray2.70B2-136[»]
    2NZDX-ray2.65A/E2-136[»]
    3B6FX-ray3.45A/E2-136[»]
    3B6GX-ray3.45A/E2-136[»]
    3C1BX-ray2.20A/E2-136[»]
    3C1CX-ray3.15A/E2-136[»]
    3GV6X-ray1.76B2-16[»]
    3KUYX-ray2.90A/E2-136[»]
    3KWQX-ray3.50A/E39-136[»]
    3KXBX-ray3.20A/E2-136[»]
    3LELX-ray2.95A/E/K/O1-136[»]
    3LJAX-ray2.75A/E2-136[»]
    3LZ0X-ray2.50A/E2-136[»]
    3LZ1X-ray2.50A/E2-136[»]
    3MGPX-ray2.44A/E2-136[»]
    3MGQX-ray2.65A/E2-136[»]
    3MGRX-ray2.30A/E2-136[»]
    3MGSX-ray3.15A/E2-136[»]
    3MNNX-ray2.50A/E2-136[»]
    3MVDX-ray2.90A/E2-136[»]
    3O62X-ray3.22A/E2-136[»]
    3REHX-ray2.50A/E2-136[»]
    3REIX-ray2.65A/E2-136[»]
    3REJX-ray2.55A/E2-136[»]
    3REKX-ray2.60A/E2-136[»]
    3RELX-ray2.70A/E2-136[»]
    3TU4X-ray3.00A/E2-136[»]
    3UT9X-ray2.20A/E2-136[»]
    3UTAX-ray2.07A/E2-136[»]
    3UTBX-ray2.20A/E2-136[»]
    4EO5X-ray2.35B62-136[»]
    4J8UX-ray2.38A/E2-136[»]
    4J8VX-ray2.58A/E2-136[»]
    4J8WX-ray2.41A/E2-136[»]
    4J8XX-ray2.87A/E2-136[»]
    4KGCX-ray2.69A/E1-136[»]
    4LD9X-ray3.31A/E1-136[»]
    ProteinModelPortaliP84233.
    SMRiP84233. Positions 17-136.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP84233.

    Family & Domainsi

    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.

    P84233-1 [UniParc]FASTAAdd to Basket

    « Hide

    MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR    50
    EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSAV MALQEASEAY 100
    LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA 136
    Length:136
    Mass (Da):15,388
    Last modified:January 23, 2007 - v2
    Checksum:i6FD8508EA50A0EEC
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X03104 Genomic DNA. Translation: CAA26890.1.
    X03017 Genomic DNA. Translation: CAA26813.1.
    X03018 Genomic DNA. Translation: CAA26818.1.
    M21286 Genomic DNA. Translation: AAA49765.1.
    M21287 Genomic DNA. Translation: AAA49770.1.
    BC133776 mRNA. Translation: AAI33777.1.
    PIRiA93596. HSXL31.
    I51448.
    RefSeqiNP_001091428.1. NM_001097959.1.
    UniGeneiXl.85517.

    Genome annotation databases

    GeneIDi100049126.
    KEGGixla:100049126.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X03104 Genomic DNA. Translation: CAA26890.1 .
    X03017 Genomic DNA. Translation: CAA26813.1 .
    X03018 Genomic DNA. Translation: CAA26818.1 .
    M21286 Genomic DNA. Translation: AAA49765.1 .
    M21287 Genomic DNA. Translation: AAA49770.1 .
    BC133776 mRNA. Translation: AAI33777.1 .
    PIRi A93596. HSXL31.
    I51448.
    RefSeqi NP_001091428.1. NM_001097959.1.
    UniGenei Xl.85517.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1F66 X-ray 2.60 A/E 1-136 [» ]
    1KX3 X-ray 2.00 A/E 2-136 [» ]
    1KX4 X-ray 2.60 A/E 2-136 [» ]
    1KX5 X-ray 1.94 A/E 2-136 [» ]
    1P34 X-ray 2.70 A/E 2-136 [» ]
    1P3A X-ray 3.00 A/E 2-136 [» ]
    1P3B X-ray 3.00 A/E 2-136 [» ]
    1P3F X-ray 2.90 A/E 2-136 [» ]
    1P3G X-ray 2.70 A/E 2-136 [» ]
    1P3I X-ray 2.30 A/E 2-136 [» ]
    1P3K X-ray 2.90 A/E 2-136 [» ]
    1P3L X-ray 2.40 A/E 2-136 [» ]
    1P3M X-ray 2.90 A/E 2-136 [» ]
    1P3O X-ray 2.75 A/E 2-136 [» ]
    1P3P X-ray 2.70 A/E 2-136 [» ]
    1S32 X-ray 2.05 A/E 2-136 [» ]
    1ZBB X-ray 9.00 A/E/a/e 2-136 [» ]
    1ZLA X-ray 2.90 A/E 2-136 [» ]
    2F8N X-ray 2.90 A/E 1-136 [» ]
    2FJ7 X-ray 3.20 A/E 2-136 [» ]
    2HUE X-ray 1.70 B 62-136 [» ]
    2IO5 X-ray 2.70 B 2-136 [» ]
    2NZD X-ray 2.65 A/E 2-136 [» ]
    3B6F X-ray 3.45 A/E 2-136 [» ]
    3B6G X-ray 3.45 A/E 2-136 [» ]
    3C1B X-ray 2.20 A/E 2-136 [» ]
    3C1C X-ray 3.15 A/E 2-136 [» ]
    3GV6 X-ray 1.76 B 2-16 [» ]
    3KUY X-ray 2.90 A/E 2-136 [» ]
    3KWQ X-ray 3.50 A/E 39-136 [» ]
    3KXB X-ray 3.20 A/E 2-136 [» ]
    3LEL X-ray 2.95 A/E/K/O 1-136 [» ]
    3LJA X-ray 2.75 A/E 2-136 [» ]
    3LZ0 X-ray 2.50 A/E 2-136 [» ]
    3LZ1 X-ray 2.50 A/E 2-136 [» ]
    3MGP X-ray 2.44 A/E 2-136 [» ]
    3MGQ X-ray 2.65 A/E 2-136 [» ]
    3MGR X-ray 2.30 A/E 2-136 [» ]
    3MGS X-ray 3.15 A/E 2-136 [» ]
    3MNN X-ray 2.50 A/E 2-136 [» ]
    3MVD X-ray 2.90 A/E 2-136 [» ]
    3O62 X-ray 3.22 A/E 2-136 [» ]
    3REH X-ray 2.50 A/E 2-136 [» ]
    3REI X-ray 2.65 A/E 2-136 [» ]
    3REJ X-ray 2.55 A/E 2-136 [» ]
    3REK X-ray 2.60 A/E 2-136 [» ]
    3REL X-ray 2.70 A/E 2-136 [» ]
    3TU4 X-ray 3.00 A/E 2-136 [» ]
    3UT9 X-ray 2.20 A/E 2-136 [» ]
    3UTA X-ray 2.07 A/E 2-136 [» ]
    3UTB X-ray 2.20 A/E 2-136 [» ]
    4EO5 X-ray 2.35 B 62-136 [» ]
    4J8U X-ray 2.38 A/E 2-136 [» ]
    4J8V X-ray 2.58 A/E 2-136 [» ]
    4J8W X-ray 2.41 A/E 2-136 [» ]
    4J8X X-ray 2.87 A/E 2-136 [» ]
    4KGC X-ray 2.69 A/E 1-136 [» ]
    4LD9 X-ray 3.31 A/E 1-136 [» ]
    ProteinModelPortali P84233.
    SMRi P84233. Positions 17-136.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 674575. 2 interactions.
    DIPi DIP-37430N.
    IntActi P84233. 4 interactions.

    Proteomic databases

    PRIDEi P84233.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 100049126.
    KEGGi xla:100049126.

    Organism-specific databases

    CTDi 126961.
    Xenbasei XB-GENE-866635. hist2h3c.

    Phylogenomic databases

    HOVERGENi HBG001172.
    KOi K11253.

    Miscellaneous databases

    EvolutionaryTracei P84233.

    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. "Individual Xenopus histone genes are replication-independent in oocytes and replication-dependent in Xenopus or mouse somatic cells."
      Old R.W., Sheikh S.A., Chambers A., Newton C.A., Mohammed A., Aldridge T.C.
      Nucleic Acids Res. 13:7341-7358(1985) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Genomic organization and nucleotide sequence of two distinct histone gene clusters from Xenopus laevis. Identification of novel conserved upstream sequence elements."
      Perry M., Thomsen G.H., Roeder R.G.
      J. Mol. Biol. 185:479-499(1985) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (GENE CLUSTERS X1H1 AND X1H3).
    3. NIH - Xenopus Gene Collection (XGC) project
      Submitted (MAR-2007) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Embryo.
    4. "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.
    5. "Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 A resolution."
      Davey C.A., Sargent D.F., Luger K., Maeder A.W., Richmond T.J.
      J. Mol. Biol. 319:1097-1113(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH H2A; H2B AND H4.

    Entry informationi

    Entry nameiH32_XENLA
    AccessioniPrimary (citable) accession number: P84233
    Secondary accession number(s): A4FVE2
    , P02295, P02297, P16105, P17269, P17320
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 85 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3