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P62799

- H4_XENLA

UniProt

P62799 - H4_XENLA

Protein

Histone H4

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.

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    DNA bindingi17 – 215

    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 H4
    OrganismiXenopus laevis (African clawed frog)
    Taxonomic identifieri8355 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

    Organism-specific databases

    XenbaseiXB-GENE-6493984. hist1h4a.

    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 – 103102Histone H4PRO_0000158376Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylserineBy similarity
    Modified residuei2 – 21PhosphoserineBy similarity
    Modified residuei4 – 41Asymmetric dimethylarginine; by PRMT1; alternateBy similarity
    Modified residuei4 – 41Citrulline; alternateBy similarity
    Modified residuei4 – 41Omega-N-methylarginine; by PRMT1; alternateBy similarity
    Modified residuei4 – 41Symmetric dimethylarginine; by PRMT5 and PRMT7; alternateBy similarity
    Modified residuei6 – 61N6-acetyllysineBy similarity
    Modified residuei9 – 91N6-acetyllysineBy similarity
    Modified residuei13 – 131N6-acetyllysineBy similarity
    Modified residuei17 – 171N6-acetyllysineBy similarity
    Modified residuei21 – 211N6,N6,N6-trimethyllysine; alternateBy similarity
    Modified residuei21 – 211N6,N6-dimethyllysine; alternateBy similarity
    Modified residuei21 – 211N6-methylated lysineBy similarity
    Modified residuei21 – 211N6-methyllysine; alternateBy similarity
    Modified residuei32 – 321N6-acetyllysineBy similarity
    Modified residuei48 – 481Phosphoserine; by PAK2By similarity
    Modified residuei52 – 521PhosphotyrosineBy similarity
    Modified residuei60 – 601N6-acetyllysineBy similarity
    Modified residuei80 – 801N6-acetyllysineBy similarity
    Modified residuei89 – 891PhosphotyrosineBy similarity
    Modified residuei92 – 921N6-acetyllysine; alternateBy similarity
    Cross-linki92 – 92Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternateBy similarity

    Post-translational modificationi

    Acetylation at Lys-6 (H4K5ac), Lys-9 (H4K8ac), Lys-13 (H4K12ac) and Lys-17 (H4K16ac) occurs in coding regions of the genome but not in heterochromatin.By similarity
    Citrullination at Arg-4 (H4R3ci) by PADI4 impairs methylation.By similarity
    Monomethylation and asymmetric dimethylation at Arg-4 (H4R3me1 and H4R3me2a, respectively) by PRMT1 favors acetylation at Lys-9 (H4K8ac) and Lys-13 (H4K12ac). Demethylation is performed by JMJD6. Symmetric dimethylation on Arg-4 (H4R3me2s) by the PRDM1/PRMT5 complex may play a crucial role in the germ-cell lineage By similarity.By similarity
    Monomethylated, dimethylated or trimethylated at Lys-21 (H4K20me1, H4K20me2, H4K20me3). Monomethylation is performed by SET8. Trimethylation is performed by SUV420H1 and SUV420H2 and induces gene silencing By similarity.By similarity
    Phosphorylated by pak2 at Ser-48 (H4S47ph). This phosphorylation increases the association of H3.3-H4 with the histone chaperone HIRA, thus promoting nucleosome assembly of H3.3-H4 and inhibiting nucleosome assembly of H3.1-H4 By similarity.By similarity
    Ubiquitinated by the CUL4-DDB-RBX1 complex in response to ultraviolet irradiation. This may weaken the interaction between histones and DNA and facilitate DNA accessibility to repair proteins. Monoubiquitinated at Lys-92 of histone H4 (H4K91ub1) in response to DNA damage. The exact role of H4K91ub1 in DNA damage response is still unclear but it may function as a licensing signal for additional histone H4 post-translational modifications such as H4 Lys-21 methylation (H4K20me) By similarity.By similarity
    Sumoylated, which is associated with transcriptional repression.By similarity

    Keywords - PTMi

    Acetylation, Citrullination, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

    Proteomic databases

    PRIDEiP62799.

    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.

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    P842332EBI-302085,EBI-350041

    Protein-protein interaction databases

    BioGridi104647. 12 interactions.
    DIPiDIP-37429N.
    IntActiP62799. 4 interactions.

    Structurei

    Secondary structure

    1
    103
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi6 – 127
    Helixi23 – 264
    Helixi27 – 293
    Helixi32 – 4110
    Beta strandi45 – 473
    Helixi51 – 7626
    Beta strandi80 – 823
    Helixi84 – 907
    Turni91 – 944
    Beta strandi96 – 1005

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1AOIX-ray2.80B/F17-103[»]
    1KX3X-ray2.00B/F2-103[»]
    1KX4X-ray2.60B/F2-103[»]
    1KX5X-ray1.94B/F2-103[»]
    1M18X-ray2.45B/F2-103[»]
    1M19X-ray2.30B/F2-103[»]
    1M1AX-ray2.65B/F2-103[»]
    1P34X-ray2.70B/F2-103[»]
    1P3AX-ray3.00B/F2-103[»]
    1P3BX-ray3.00B/F2-103[»]
    1P3FX-ray2.90B/F2-103[»]
    1P3GX-ray2.70B/F2-103[»]
    1P3IX-ray2.30B/F2-103[»]
    1P3KX-ray2.90B/F2-103[»]
    1P3LX-ray2.40B/F2-103[»]
    1P3MX-ray2.90B/F2-103[»]
    1P3OX-ray2.75B/F2-103[»]
    1P3PX-ray2.70B/F2-103[»]
    1S32X-ray2.05B/F2-103[»]
    1ZBBX-ray9.00B/F/b/f2-103[»]
    1ZLAX-ray2.90B/F2-103[»]
    2F8NX-ray2.90B/F1-103[»]
    2FJ7X-ray3.20B/F2-103[»]
    2HUEX-ray1.70C21-103[»]
    2IO5X-ray2.70C2-103[»]
    2NZDX-ray2.65B/F2-103[»]
    3B6FX-ray3.45B/F2-103[»]
    3B6GX-ray3.45B/F2-103[»]
    3C1BX-ray2.20B/F2-103[»]
    3C1CX-ray3.15B/F2-103[»]
    3KUYX-ray2.90B/F2-103[»]
    3KWQX-ray3.50B/F21-103[»]
    3KXBX-ray3.20B/F2-103[»]
    3LELX-ray2.95B/F/L/P2-103[»]
    3LJAX-ray2.75B/F2-103[»]
    3LZ0X-ray2.50B/F2-103[»]
    3LZ1X-ray2.50B/F2-103[»]
    3MGPX-ray2.44B/F2-103[»]
    3MGQX-ray2.65B/F2-103[»]
    3MGRX-ray2.30B/F2-103[»]
    3MGSX-ray3.15B/F2-103[»]
    3MNNX-ray2.50B/F2-103[»]
    3MVDX-ray2.90B/F2-103[»]
    3O62X-ray3.22B/F2-103[»]
    3REHX-ray2.50B/F2-103[»]
    3REIX-ray2.65B/F2-103[»]
    3REJX-ray2.55B/F2-103[»]
    3REKX-ray2.60B/F2-103[»]
    3RELX-ray2.70B/F2-103[»]
    3TU4X-ray3.00B/F2-103[»]
    3UT9X-ray2.20B/F2-103[»]
    3UTAX-ray2.07B/F2-103[»]
    3UTBX-ray2.20B/F2-103[»]
    4EO5X-ray2.35C21-103[»]
    4J8UX-ray2.38B/F2-103[»]
    4J8VX-ray2.58B/F2-103[»]
    4J8WX-ray2.41B/F2-103[»]
    4J8XX-ray2.87B/F2-103[»]
    4KGCX-ray2.69B/F1-103[»]
    4LD9X-ray3.31B/F1-103[»]
    ProteinModelPortaliP62799.
    SMRiP62799. Positions 21-102.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP62799.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the histone H4 family.Curated

    Phylogenomic databases

    HOVERGENiHBG051878.
    KOiK11254.

    Family and domain databases

    Gene3Di1.10.20.10. 1 hit.
    InterProiIPR009072. Histone-fold.
    IPR007125. Histone_core_D.
    IPR001951. Histone_H4.
    IPR019809. Histone_H4_CS.
    [Graphical view]
    PfamiPF00125. Histone. 1 hit.
    [Graphical view]
    PRINTSiPR00623. HISTONEH4.
    SMARTiSM00417. H4. 1 hit.
    [Graphical view]
    SUPFAMiSSF47113. SSF47113. 1 hit.
    PROSITEiPS00047. HISTONE_H4. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P62799-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL    50
    IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG 100
    FGG 103
    Length:103
    Mass (Da):11,367
    Last modified:January 23, 2007 - v2
    Checksum:iA9E5DFD3F8B97598
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X00224 Genomic DNA. Translation: CAA25042.1.
    X03017 Genomic DNA. Translation: CAA26809.1.
    X03017 Genomic DNA. Translation: CAA26814.1.
    X03018 Genomic DNA. Translation: CAA26819.1.
    M21286 Genomic DNA. Translation: AAA49761.1.
    M21286 Genomic DNA. Translation: AAA49766.1.
    M21287 Genomic DNA. Translation: AAA49771.1.
    BC078038 mRNA. Translation: AAH78038.1.
    PIRiA02641. HSXL4.
    RefSeqiNP_001087926.1. NM_001094457.1.
    UniGeneiXl.85592.

    Genome annotation databases

    GeneIDi447787.
    KEGGixla:447787.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X00224 Genomic DNA. Translation: CAA25042.1 .
    X03017 Genomic DNA. Translation: CAA26809.1 .
    X03017 Genomic DNA. Translation: CAA26814.1 .
    X03018 Genomic DNA. Translation: CAA26819.1 .
    M21286 Genomic DNA. Translation: AAA49761.1 .
    M21286 Genomic DNA. Translation: AAA49766.1 .
    M21287 Genomic DNA. Translation: AAA49771.1 .
    BC078038 mRNA. Translation: AAH78038.1 .
    PIRi A02641. HSXL4.
    RefSeqi NP_001087926.1. NM_001094457.1.
    UniGenei Xl.85592.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1AOI X-ray 2.80 B/F 17-103 [» ]
    1KX3 X-ray 2.00 B/F 2-103 [» ]
    1KX4 X-ray 2.60 B/F 2-103 [» ]
    1KX5 X-ray 1.94 B/F 2-103 [» ]
    1M18 X-ray 2.45 B/F 2-103 [» ]
    1M19 X-ray 2.30 B/F 2-103 [» ]
    1M1A X-ray 2.65 B/F 2-103 [» ]
    1P34 X-ray 2.70 B/F 2-103 [» ]
    1P3A X-ray 3.00 B/F 2-103 [» ]
    1P3B X-ray 3.00 B/F 2-103 [» ]
    1P3F X-ray 2.90 B/F 2-103 [» ]
    1P3G X-ray 2.70 B/F 2-103 [» ]
    1P3I X-ray 2.30 B/F 2-103 [» ]
    1P3K X-ray 2.90 B/F 2-103 [» ]
    1P3L X-ray 2.40 B/F 2-103 [» ]
    1P3M X-ray 2.90 B/F 2-103 [» ]
    1P3O X-ray 2.75 B/F 2-103 [» ]
    1P3P X-ray 2.70 B/F 2-103 [» ]
    1S32 X-ray 2.05 B/F 2-103 [» ]
    1ZBB X-ray 9.00 B/F/b/f 2-103 [» ]
    1ZLA X-ray 2.90 B/F 2-103 [» ]
    2F8N X-ray 2.90 B/F 1-103 [» ]
    2FJ7 X-ray 3.20 B/F 2-103 [» ]
    2HUE X-ray 1.70 C 21-103 [» ]
    2IO5 X-ray 2.70 C 2-103 [» ]
    2NZD X-ray 2.65 B/F 2-103 [» ]
    3B6F X-ray 3.45 B/F 2-103 [» ]
    3B6G X-ray 3.45 B/F 2-103 [» ]
    3C1B X-ray 2.20 B/F 2-103 [» ]
    3C1C X-ray 3.15 B/F 2-103 [» ]
    3KUY X-ray 2.90 B/F 2-103 [» ]
    3KWQ X-ray 3.50 B/F 21-103 [» ]
    3KXB X-ray 3.20 B/F 2-103 [» ]
    3LEL X-ray 2.95 B/F/L/P 2-103 [» ]
    3LJA X-ray 2.75 B/F 2-103 [» ]
    3LZ0 X-ray 2.50 B/F 2-103 [» ]
    3LZ1 X-ray 2.50 B/F 2-103 [» ]
    3MGP X-ray 2.44 B/F 2-103 [» ]
    3MGQ X-ray 2.65 B/F 2-103 [» ]
    3MGR X-ray 2.30 B/F 2-103 [» ]
    3MGS X-ray 3.15 B/F 2-103 [» ]
    3MNN X-ray 2.50 B/F 2-103 [» ]
    3MVD X-ray 2.90 B/F 2-103 [» ]
    3O62 X-ray 3.22 B/F 2-103 [» ]
    3REH X-ray 2.50 B/F 2-103 [» ]
    3REI X-ray 2.65 B/F 2-103 [» ]
    3REJ X-ray 2.55 B/F 2-103 [» ]
    3REK X-ray 2.60 B/F 2-103 [» ]
    3REL X-ray 2.70 B/F 2-103 [» ]
    3TU4 X-ray 3.00 B/F 2-103 [» ]
    3UT9 X-ray 2.20 B/F 2-103 [» ]
    3UTA X-ray 2.07 B/F 2-103 [» ]
    3UTB X-ray 2.20 B/F 2-103 [» ]
    4EO5 X-ray 2.35 C 21-103 [» ]
    4J8U X-ray 2.38 B/F 2-103 [» ]
    4J8V X-ray 2.58 B/F 2-103 [» ]
    4J8W X-ray 2.41 B/F 2-103 [» ]
    4J8X X-ray 2.87 B/F 2-103 [» ]
    4KGC X-ray 2.69 B/F 1-103 [» ]
    4LD9 X-ray 3.31 B/F 1-103 [» ]
    ProteinModelPortali P62799.
    SMRi P62799. Positions 21-102.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 104647. 12 interactions.
    DIPi DIP-37429N.
    IntActi P62799. 4 interactions.

    Proteomic databases

    PRIDEi P62799.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 447787.
    KEGGi xla:447787.

    Organism-specific databases

    CTDi 8359.
    Xenbasei XB-GENE-6493984. hist1h4a.

    Phylogenomic databases

    HOVERGENi HBG051878.
    KOi K11254.

    Miscellaneous databases

    EvolutionaryTracei P62799.

    Family and domain databases

    Gene3Di 1.10.20.10. 1 hit.
    InterProi IPR009072. Histone-fold.
    IPR007125. Histone_core_D.
    IPR001951. Histone_H4.
    IPR019809. Histone_H4_CS.
    [Graphical view ]
    Pfami PF00125. Histone. 1 hit.
    [Graphical view ]
    PRINTSi PR00623. HISTONEH4.
    SMARTi SM00417. H4. 1 hit.
    [Graphical view ]
    SUPFAMi SSF47113. SSF47113. 1 hit.
    PROSITEi PS00047. HISTONE_H4. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Primary structure of the histone H3 and H4 genes and their flanking sequences in a minor histone gene cluster of Xenopus laevis."
      Moorman A.F.M., de Boer P.A.J., de Laaf R.T.M., van Dongen W.M.A.M., Destree O.H.J.
      FEBS Lett. 136:45-52(1981) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Transcription of a cloned Xenopus laevis H4 histone gene in the homologous frog oocyte system depends on an evolutionary conserved sequence motif in the -50 region."
      Clerc R.G., Bucher P., Strub K., Birnstiel M.L.
      Nucleic Acids Res. 11:8641-8657(1983) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    3. "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].
    4. NIH - Xenopus Gene Collection (XGC) project
      Submitted (JUL-2004) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Embryo.
    5. "Crystal structure of the nucleosome core particle at 2.8 A resolution."
      Luger K., Mader A.W., Richmond R.K., Sargent D.F., Richmond T.J.
      Nature 389:251-260(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 17-103.

    Entry informationi

    Entry nameiH4_XENLA
    AccessioniPrimary (citable) accession number: P62799
    Secondary accession number(s): P02304, P02305, Q6AZG5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 99 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