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P02281

- H2B11_XENLA

UniProt

P02281 - H2B11_XENLA

Protein

Histone H2B 1.1

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

    GO - Biological processi

    1. nucleosome assembly Source: InterPro

    Keywords - Ligandi

    DNA-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Histone H2B 1.1
    Short name:
    H2B1.1
    OrganismiXenopus laevis (African clawed frog)
    Taxonomic identifieri8355 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

    Organism-specific databases

    XenbaseiXB-GENE-6493994. hist1h2bj.

    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 – 126125Histone H2B 1.1PRO_0000071854Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei6 – 61N6-acetyllysineBy similarity
    Modified residuei13 – 131N6-acetyllysineBy similarity
    Modified residuei15 – 151Phosphoserine1 Publication
    Modified residuei16 – 161N6-acetyllysineBy similarity
    Modified residuei21 – 211N6-acetyllysineBy similarity
    Glycosylationi113 – 1131O-linked (GlcNAc)By similarity
    Cross-linki121 – 121Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity

    Post-translational modificationi

    Monoubiquitination of Lys-121 by BRE1 gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 'Lys-4' and 'Lys-79' methylation.By similarity
    Phosphorylated on Ser-15 during developmentally programmed apoptosis; which may facilitate apoptotic chromatin condensation.1 Publication
    GlcNAcylation at Ser-113 promotes monoubiquitination of Lys-121. It fluctuates in response to extracellular glucose, and associates with transcribed genes By similarity.By similarity

    Keywords - PTMi

    Acetylation, Glycoprotein, Isopeptide bond, Phosphoprotein, Ubl conjugation

    Proteomic databases

    PRIDEiP02281.

    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.3 Publications

    Protein-protein interaction databases

    BioGridi103448. 6 interactions.
    DIPiDIP-38577N.
    IntActiP02281. 3 interactions.

    Structurei

    Secondary structure

    1
    126
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi9 – 113
    Beta strandi18 – 203
    Helixi39 – 4911
    Helixi57 – 8428
    Beta strandi88 – 903
    Helixi92 – 10211
    Helixi105 – 12319

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1AOIX-ray2.80D/H28-126[»]
    1F66X-ray2.60D/H1-126[»]
    1KX3X-ray2.00D/H2-126[»]
    1KX4X-ray2.60D/H2-126[»]
    1KX5X-ray1.94D/H2-126[»]
    1M18X-ray2.45D/H2-126[»]
    1M19X-ray2.30D/H2-126[»]
    1M1AX-ray2.65D/H2-126[»]
    1P34X-ray2.70D/H2-126[»]
    1P3AX-ray3.00D/H2-126[»]
    1P3BX-ray3.00D/H2-126[»]
    1P3FX-ray2.90D/H2-126[»]
    1P3GX-ray2.70D/H2-126[»]
    1P3IX-ray2.30D/H2-126[»]
    1P3KX-ray2.90D/H2-126[»]
    1P3LX-ray2.40D/H2-126[»]
    1P3MX-ray2.90D/H2-126[»]
    1P3OX-ray2.75D/H2-126[»]
    1P3PX-ray2.70D/H2-126[»]
    1S32X-ray2.05D/H5-126[»]
    1ZBBX-ray9.00D/H/d/h2-126[»]
    1ZLAX-ray2.90D/H2-126[»]
    2F8NX-ray2.90H5-126[»]
    2FJ7X-ray3.20D/H2-126[»]
    2NZDX-ray2.65D/H2-126[»]
    3B6FX-ray3.45D/H2-126[»]
    3B6GX-ray3.45D/H2-126[»]
    3KUYX-ray2.90D/H2-126[»]
    3KWQX-ray3.50D/H34-126[»]
    3KXBX-ray3.20D/H5-126[»]
    3LELX-ray2.95D/H/N/R2-126[»]
    3LJAX-ray2.75D/H5-126[»]
    3LZ0X-ray2.50D/H2-126[»]
    3LZ1X-ray2.50D/H2-126[»]
    3MGPX-ray2.44D/H2-126[»]
    3MGQX-ray2.65D/H2-126[»]
    3MGRX-ray2.30D/H2-126[»]
    3MGSX-ray3.15D/H2-126[»]
    3MNNX-ray2.50D/H2-126[»]
    3MVDX-ray2.90D/H5-126[»]
    3O62X-ray3.22D/H5-126[»]
    3REHX-ray2.50D/H5-126[»]
    3REIX-ray2.65D/H5-126[»]
    3REJX-ray2.55D/H5-126[»]
    3REKX-ray2.60D/H5-126[»]
    3RELX-ray2.70D/H5-126[»]
    3TU4X-ray3.00D/H5-126[»]
    3UT9X-ray2.20D/H2-126[»]
    3UTAX-ray2.07D/H2-126[»]
    3UTBX-ray2.20D/H2-126[»]
    4J8UX-ray2.38D/H2-126[»]
    4J8VX-ray2.58D/H2-126[»]
    4J8WX-ray2.41D/H2-126[»]
    4J8XX-ray2.87D/H2-126[»]
    4KGCX-ray2.69D/H1-126[»]
    4KHAX-ray2.35A34-126[»]
    4LD9X-ray3.31D/H1-126[»]
    ProteinModelPortaliP02281.
    SMRiP02281. Positions 5-126.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP02281.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the histone H2B family.Curated

    Phylogenomic databases

    HOVERGENiHBG007774.
    KOiK11252.

    Family and domain databases

    Gene3Di1.10.20.10. 1 hit.
    InterProiIPR009072. Histone-fold.
    IPR007125. Histone_core_D.
    IPR000558. Histone_H2B.
    [Graphical view]
    PANTHERiPTHR23428. PTHR23428. 1 hit.
    PfamiPF00125. Histone. 1 hit.
    [Graphical view]
    PRINTSiPR00621. HISTONEH2B.
    SMARTiSM00427. H2B. 1 hit.
    [Graphical view]
    SUPFAMiSSF47113. SSF47113. 1 hit.
    PROSITEiPS00357. HISTONE_H2B. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P02281-1 [UniParc]FASTAAdd to Basket

    « Hide

    MPEPAKSAPA PKKGSKKAVT KTQKKDGKKR RKSRKESYAI YVYKVLKQVH    50
    PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRSTI TSREIQTAVR 100
    LLLPGELAKH AVSEGTKAVT KYTSAK 126
    Length:126
    Mass (Da):13,934
    Last modified:January 23, 2007 - v2
    Checksum:iDA6C122EC8359FD9
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X03018 Genomic DNA. Translation: CAA26816.1.
    M21287 Genomic DNA. Translation: AAA49768.1.
    BC077399 mRNA. Translation: AAH77399.1.
    PIRiB92918. HSXLB1.
    RefSeqiNP_001086753.1. NM_001093284.1.
    UniGeneiXl.46757.

    Genome annotation databases

    GeneIDi446588.
    KEGGixla:446588.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X03018 Genomic DNA. Translation: CAA26816.1 .
    M21287 Genomic DNA. Translation: AAA49768.1 .
    BC077399 mRNA. Translation: AAH77399.1 .
    PIRi B92918. HSXLB1.
    RefSeqi NP_001086753.1. NM_001093284.1.
    UniGenei Xl.46757.

    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 D/H 28-126 [» ]
    1F66 X-ray 2.60 D/H 1-126 [» ]
    1KX3 X-ray 2.00 D/H 2-126 [» ]
    1KX4 X-ray 2.60 D/H 2-126 [» ]
    1KX5 X-ray 1.94 D/H 2-126 [» ]
    1M18 X-ray 2.45 D/H 2-126 [» ]
    1M19 X-ray 2.30 D/H 2-126 [» ]
    1M1A X-ray 2.65 D/H 2-126 [» ]
    1P34 X-ray 2.70 D/H 2-126 [» ]
    1P3A X-ray 3.00 D/H 2-126 [» ]
    1P3B X-ray 3.00 D/H 2-126 [» ]
    1P3F X-ray 2.90 D/H 2-126 [» ]
    1P3G X-ray 2.70 D/H 2-126 [» ]
    1P3I X-ray 2.30 D/H 2-126 [» ]
    1P3K X-ray 2.90 D/H 2-126 [» ]
    1P3L X-ray 2.40 D/H 2-126 [» ]
    1P3M X-ray 2.90 D/H 2-126 [» ]
    1P3O X-ray 2.75 D/H 2-126 [» ]
    1P3P X-ray 2.70 D/H 2-126 [» ]
    1S32 X-ray 2.05 D/H 5-126 [» ]
    1ZBB X-ray 9.00 D/H/d/h 2-126 [» ]
    1ZLA X-ray 2.90 D/H 2-126 [» ]
    2F8N X-ray 2.90 H 5-126 [» ]
    2FJ7 X-ray 3.20 D/H 2-126 [» ]
    2NZD X-ray 2.65 D/H 2-126 [» ]
    3B6F X-ray 3.45 D/H 2-126 [» ]
    3B6G X-ray 3.45 D/H 2-126 [» ]
    3KUY X-ray 2.90 D/H 2-126 [» ]
    3KWQ X-ray 3.50 D/H 34-126 [» ]
    3KXB X-ray 3.20 D/H 5-126 [» ]
    3LEL X-ray 2.95 D/H/N/R 2-126 [» ]
    3LJA X-ray 2.75 D/H 5-126 [» ]
    3LZ0 X-ray 2.50 D/H 2-126 [» ]
    3LZ1 X-ray 2.50 D/H 2-126 [» ]
    3MGP X-ray 2.44 D/H 2-126 [» ]
    3MGQ X-ray 2.65 D/H 2-126 [» ]
    3MGR X-ray 2.30 D/H 2-126 [» ]
    3MGS X-ray 3.15 D/H 2-126 [» ]
    3MNN X-ray 2.50 D/H 2-126 [» ]
    3MVD X-ray 2.90 D/H 5-126 [» ]
    3O62 X-ray 3.22 D/H 5-126 [» ]
    3REH X-ray 2.50 D/H 5-126 [» ]
    3REI X-ray 2.65 D/H 5-126 [» ]
    3REJ X-ray 2.55 D/H 5-126 [» ]
    3REK X-ray 2.60 D/H 5-126 [» ]
    3REL X-ray 2.70 D/H 5-126 [» ]
    3TU4 X-ray 3.00 D/H 5-126 [» ]
    3UT9 X-ray 2.20 D/H 2-126 [» ]
    3UTA X-ray 2.07 D/H 2-126 [» ]
    3UTB X-ray 2.20 D/H 2-126 [» ]
    4J8U X-ray 2.38 D/H 2-126 [» ]
    4J8V X-ray 2.58 D/H 2-126 [» ]
    4J8W X-ray 2.41 D/H 2-126 [» ]
    4J8X X-ray 2.87 D/H 2-126 [» ]
    4KGC X-ray 2.69 D/H 1-126 [» ]
    4KHA X-ray 2.35 A 34-126 [» ]
    4LD9 X-ray 3.31 D/H 1-126 [» ]
    ProteinModelPortali P02281.
    SMRi P02281. Positions 5-126.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 103448. 6 interactions.
    DIPi DIP-38577N.
    IntActi P02281. 3 interactions.

    Proteomic databases

    PRIDEi P02281.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 446588.
    KEGGi xla:446588.

    Organism-specific databases

    CTDi 8970.
    Xenbasei XB-GENE-6493994. hist1h2bj.

    Phylogenomic databases

    HOVERGENi HBG007774.
    KOi K11252.

    Miscellaneous databases

    EvolutionaryTracei P02281.

    Family and domain databases

    Gene3Di 1.10.20.10. 1 hit.
    InterProi IPR009072. Histone-fold.
    IPR007125. Histone_core_D.
    IPR000558. Histone_H2B.
    [Graphical view ]
    PANTHERi PTHR23428. PTHR23428. 1 hit.
    Pfami PF00125. Histone. 1 hit.
    [Graphical view ]
    PRINTSi PR00621. HISTONEH2B.
    SMARTi SM00427. H2B. 1 hit.
    [Graphical view ]
    SUPFAMi SSF47113. SSF47113. 1 hit.
    PROSITEi PS00357. HISTONE_H2B. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "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 CLUSTER X1H3).
    2. NIH - Xenopus Gene Collection (XGC) project
      Submitted (JUL-2004) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Embryo.
    3. "Histone H2B variants from the erythrocytes of an amphibian, a reptile and a bird."
      van Helden P., Strickland W.N., Brandt W.F., von Holt C.
      Biochim. Biophys. Acta 533:278-281(1978) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-30 AND 63-85.
      Tissue: Erythrocyte.
    4. "Apoptotic phosphorylation of histone H2B is mediated by mammalian sterile twenty kinase."
      Cheung W.L., Ajiro K., Samejima K., Kloc M., Cheung P., Mizzen C.A., Beeser A., Etkin L.D., Chernoff J., Earnshaw W.C., Allis C.D.
      Cell 113:507-517(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION AT SER-15.
    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 NUCLEOSOME CORE COMPLEX, SUBUNIT.
    6. "Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands."
      Suto R.K., Edayathumangalam R.S., White C.L., Melander C., Gottesfeld J.M., Dervan P.B., Luger K.
      J. Mol. Biol. 326:371-380(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF NUCLEOSOME CORE COMPLEX, SUBUNIT.
    7. "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions."
      Muthurajan U.M., Bao Y., Forsberg L.J., Edayathumangalam R.S., Dyer P.N., White C.L., Luger K.
      EMBO J. 23:260-271(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF NUCLEOSOME CORE COMPLEX, SUBUNIT.

    Entry informationi

    Entry nameiH2B11_XENLA
    AccessioniPrimary (citable) accession number: P02281
    Secondary accession number(s): Q6AZT0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 116 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, Direct protein sequencing

    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