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P84229

- H32_CHICK

UniProt

P84229 - H32_CHICK

Protein

Histone H3.2

Gene

H3-I

more
Organism
Gallus gallus (Chicken)
Status
Reviewed - Annotation score: 5 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.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei37 – 382Involved in HMGB1-binding

    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_189773. RNA Polymerase I Chain Elongation.
    REACT_194991. Oxidative Stress Induced Senescence.
    REACT_197049. Amyloids.
    REACT_197541. Factors involved in megakaryocyte development and platelet production.
    REACT_204005. PRC2 methylates histones and DNA.
    REACT_214700. Senescence-Associated Secretory Phenotype (SASP).
    REACT_223091. SIRT1 negatively regulates rRNA Expression.
    REACT_223355. NoRC negatively regulates rRNA expression.
    REACT_224340. RNA Polymerase I Promoter Opening.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Histone H3.2
    Alternative name(s):
    Histone H3 class I
    Gene namesi
    Name:H3-I
    AND
    Name:H3-II
    AND
    Name:H3-III
    AND
    Name:H3-IV
    AND
    Name:H3-V
    AND
    Name:H3-VI
    AND
    Name:H3-VII
    AND
    Name:H3-VIII
    OrganismiGallus gallus (Chicken)
    Taxonomic identifieri9031 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiTestudines + Archosauria groupArchosauriaDinosauriaSaurischiaTheropodaCoelurosauriaAvesNeognathaeGalliformesPhasianidaePhasianinaeGallus
    ProteomesiUP000000539: Chromosome 1

    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 – 11Removed1 Publication
    Chaini2 – 136135Histone H3.2PRO_0000221260Add
    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-methyllysine1 Publication
    Modified residuei7 – 71Phosphothreonine; by PKCBy similarity
    Modified residuei10 – 101N6,N6,N6-trimethyllysine; alternate1 Publication
    Modified residuei10 – 101N6,N6-dimethyllysine; alternate1 Publication
    Modified residuei10 – 101N6-methyllysine; alternate1 Publication
    Modified residuei11 – 111Phosphoserine; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5By similarity
    Modified residuei12 – 121Phosphothreonine; by PKCBy similarity
    Modified residuei15 – 151N6,N6-dimethyllysine; alternate1 Publication
    Modified residuei15 – 151N6-acetyllysine; alternate1 Publication
    Modified residuei18 – 181Asymmetric dimethylarginineBy similarity
    Modified residuei19 – 191N6-acetyllysine; alternate1 Publication
    Modified residuei19 – 191N6-methylated lysine; alternateBy similarity
    Modified residuei24 – 241N6-acetyllysine1 Publication
    Modified residuei28 – 281N6-acetyllysine; alternateBy similarity
    Modified residuei28 – 281N6-methylated lysine; alternate1 Publication
    Modified residuei29 – 291Phosphoserine; by AURKB, AURKC and RPS6KA5By similarity
    Modified residuei37 – 371N6-acetyllysine; alternateBy similarity
    Modified residuei37 – 371N6-methylated lysine; alternate1 Publication
    Modified residuei42 – 421PhosphotyrosineBy similarity
    Modified residuei58 – 581PhosphoserineBy similarity
    Modified residuei65 – 651N6-methylated lysineBy similarity
    Modified residuei80 – 801N6,N6-dimethyllysine; alternate1 Publication
    Modified residuei80 – 801N6-methyllysine; alternate1 Publication
    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 Probable. 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 similarityCurated
    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' Probable.1 Publication
    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

    PaxDbiP84229.
    PRIDEiP84229.

    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 HMGB1.3 Publications

    Protein-protein interaction databases

    BioGridi687084. 4 interactions.
    IntActiP84229. 3 interactions.
    STRINGi9031.ENSGALP00000019185.

    Structurei

    Secondary structure

    1
    136
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi34 – 374
    Helixi44 – 5714
    Helixi65 – 7915
    Beta strandi80 – 823
    Helixi87 – 11428
    Beta strandi118 – 1203
    Helixi122 – 13110

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1EQZX-ray2.50C/G1-136[»]
    1HIOX-ray3.10C44-136[»]
    1HQ3X-ray2.15C/G1-136[»]
    1TZYX-ray1.90C/G1-136[»]
    2AROX-ray2.10C/G1-136[»]
    2HIOX-ray3.10C1-136[»]
    3C9Kelectron microscopy20.00C/G2-136[»]
    ProteinModelPortaliP84229.
    SMRiP84229. Positions 17-136.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP84229.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the histone H3 family.Curated

    Phylogenomic databases

    eggNOGiCOG2036.
    GeneTreeiENSGT00750000117468.
    HOGENOMiHOG000155290.
    HOVERGENiHBG001172.
    InParanoidiP84229.
    KOiK11253.
    PhylomeDBiP84229.
    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.

    P84229-1 [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
    X02218 Genomic DNA. Translation: CAA26138.1.
    J00869 Genomic DNA. Translation: AAA48795.1. Sequence problems.
    M61154 Genomic DNA. Translation: AAA48796.1.
    M61155 Genomic DNA. Translation: AAA48797.1.
    X62291 Genomic DNA. Translation: CAA44180.1.
    X62292 Genomic DNA. Translation: CAA44181.1.
    U37577 Genomic DNA. Translation: AAC60003.1.
    U37578 Genomic DNA. Translation: AAC60004.1.
    U37579 Genomic DNA. Translation: AAC60005.1.
    PIRiS18716. HSCH3.
    RefSeqiNP_001268409.1. NM_001281480.1.
    NP_001268438.1. NM_001281509.1.
    XP_001232833.1. XM_001232832.3.
    XP_001233028.1. XM_001233027.3.
    XP_004937729.1. XM_004937672.1.
    XP_416193.2. XM_416193.3.
    UniGeneiGga.5274.

    Genome annotation databases

    EnsembliENSGALT00000042655; ENSGALP00000042290; ENSGALG00000027064.
    ENSGALT00000043934; ENSGALP00000040958; ENSGALG00000027257.
    GeneIDi100858681.
    417953.
    768333.
    769809.
    769852.
    770022.
    KEGGigga:100858681.
    gga:417953.
    gga:768333.
    gga:769809.
    gga:769852.
    gga:770022.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X02218 Genomic DNA. Translation: CAA26138.1 .
    J00869 Genomic DNA. Translation: AAA48795.1 . Sequence problems.
    M61154 Genomic DNA. Translation: AAA48796.1 .
    M61155 Genomic DNA. Translation: AAA48797.1 .
    X62291 Genomic DNA. Translation: CAA44180.1 .
    X62292 Genomic DNA. Translation: CAA44181.1 .
    U37577 Genomic DNA. Translation: AAC60003.1 .
    U37578 Genomic DNA. Translation: AAC60004.1 .
    U37579 Genomic DNA. Translation: AAC60005.1 .
    PIRi S18716. HSCH3.
    RefSeqi NP_001268409.1. NM_001281480.1.
    NP_001268438.1. NM_001281509.1.
    XP_001232833.1. XM_001232832.3.
    XP_001233028.1. XM_001233027.3.
    XP_004937729.1. XM_004937672.1.
    XP_416193.2. XM_416193.3.
    UniGenei Gga.5274.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1EQZ X-ray 2.50 C/G 1-136 [» ]
    1HIO X-ray 3.10 C 44-136 [» ]
    1HQ3 X-ray 2.15 C/G 1-136 [» ]
    1TZY X-ray 1.90 C/G 1-136 [» ]
    2ARO X-ray 2.10 C/G 1-136 [» ]
    2HIO X-ray 3.10 C 1-136 [» ]
    3C9K electron microscopy 20.00 C/G 2-136 [» ]
    ProteinModelPortali P84229.
    SMRi P84229. Positions 17-136.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 687084. 4 interactions.
    IntActi P84229. 3 interactions.
    STRINGi 9031.ENSGALP00000019185.

    Proteomic databases

    PaxDbi P84229.
    PRIDEi P84229.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSGALT00000042655 ; ENSGALP00000042290 ; ENSGALG00000027064 .
    ENSGALT00000043934 ; ENSGALP00000040958 ; ENSGALG00000027257 .
    GeneIDi 100858681.
    417953.
    768333.
    769809.
    769852.
    770022.
    KEGGi gga:100858681.
    gga:417953.
    gga:768333.
    gga:769809.
    gga:769852.
    gga:770022.

    Phylogenomic databases

    eggNOGi COG2036.
    GeneTreei ENSGT00750000117468.
    HOGENOMi HOG000155290.
    HOVERGENi HBG001172.
    InParanoidi P84229.
    KOi K11253.
    PhylomeDBi P84229.
    TreeFami TF314241.

    Enzyme and pathway databases

    Reactomei REACT_189773. RNA Polymerase I Chain Elongation.
    REACT_194991. Oxidative Stress Induced Senescence.
    REACT_197049. Amyloids.
    REACT_197541. Factors involved in megakaryocyte development and platelet production.
    REACT_204005. PRC2 methylates histones and DNA.
    REACT_214700. Senescence-Associated Secretory Phenotype (SASP).
    REACT_223091. SIRT1 negatively regulates rRNA Expression.
    REACT_223355. NoRC negatively regulates rRNA expression.
    REACT_224340. RNA Polymerase I Promoter Opening.

    Miscellaneous databases

    EvolutionaryTracei P84229.
    NextBioi 20821179.

    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. "Inverted duplication of histone genes in chicken and disposition of regulatory sequences."
      Wang S.W., Robins A.J., D'Andrea R., Wells J.R.E.
      Nucleic Acids Res. 13:1369-1387(1985) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "A chicken histone H3 gene contains intervening sequences."
      Engel J.D., Sugarman B.J., Dodgson J.B.
      Nature 297:434-436(1982) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    3. "Nucleotide sequences of two members of the chicken H3 histone-encoding gene family."
      Nakayama T.
      Gene 102:289-290(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (H3-II AND H3-III).
    4. "Nucleotide sequences of new members (H3-IV and H3-V) of the chicken H3 histone-encoding gene family."
      Setoguchi Y., Nakayama T.
      Nucleic Acids Res. 19:6327-6327(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (H3-IV AND H3-V).
      Strain: White leghorn.
    5. "Organization of the chicken histone genes in a major gene cluster and generation of an almost complete set of the core histone protein sequences."
      Takami Y., Higashio M., Fukuoka T., Takechi S., Nakayama T.
      DNA Res. 3:95-99(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (H3-VI; H3-VII AND H3-VIII).
      Strain: White leghorn.
      Tissue: Liver.
    6. "The determination of the primary structure of histone F3 from chicken erythrocytes by automatic Edman degradation. 2. Sequence analysis of histone F3."
      Brandt W.F., von Holt C.
      Eur. J. Biochem. 46:419-429(1974) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-136.
    7. "Identification of acetylation and methylation sites of histone H3 from chicken erythrocytes by high-accuracy matrix-assisted laser desorption ionization-time-of-flight, matrix-assisted laser desorption ionization-postsource decay, and nanoelectrospray ionization tandem mass spectrometry."
      Zhang K., Tang H., Huang L., Blankenship J.W., Jones P.R., Xiang F., Yau P.M., Burlingame A.L.
      Anal. Biochem. 306:259-269(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: METHYLATION AT LYS-5; LYS-10; LYS-15; LYS-28; LYS-37 AND LYS-80, ACETYLATION AT LYS-15; LYS-19 AND LYS-24, IDENTIFICATION BY MASS SPECTROMETRY.
    8. "Distinct domains in HMGB1 are involved in specific intramolecular and nucleosomal interactions."
      Kawase T., Sato K., Ueda T., Yoshida M.
      Biochemistry 47:13991-13996(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH HMGB1.
    9. "The nucleosomal core histone octamer at 3.1 A resolution: a tripartite protein assembly and a left-handed superhelix."
      Arents G., Burlingame R.W., Wang B.-C., Love W.E., Moudrianakis E.N.
      Proc. Natl. Acad. Sci. U.S.A. 88:10148-10152(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS).
    10. "Asymmetries in the nucleosome core particle at 2.5 A resolution."
      Harp J.M., Hanson B.L., Timm D.E., Bunick G.J.
      Acta Crystallogr. D 56:1513-1534(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH H2A; H2B AND H4.
    11. "Structure of the histone-core octamer in KCl/phosphate crystals at 2.15 A resolution."
      Chantalat L., Nicholson J.M., Lambert S.J., Reid A.J., Donovan M.J., Reynolds C.D., Wood C.M., Baldwin J.P.
      Acta Crystallogr. D 59:1395-1407(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) IN COMPLEX WITH H2A AND H2B.

    Entry informationi

    Entry nameiH32_CHICK
    AccessioniPrimary (citable) accession number: P84229
    Secondary accession number(s): 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 95 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, Complete proteome, Direct protein sequencing, Reference proteome

    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