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Q02874

- H2AY_RAT

UniProt

Q02874 - H2AY_RAT

Protein

Core histone macro-H2A.1

Gene

H2afy

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 124 (01 Oct 2014)
      Sequence version 4 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Variant histone H2A which replaces conventional H2A in a subset of nucleosomes where it represses transcription. 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. Involved in stable X chromosome inactivation. Inhibits the binding of transcription factors and interferes with the activity of remodeling SWI/SNF complexes. Inhibits histone acetylation by EP300 and recruits class I HDACs, which induces a hypoacetylated state of chromatin. In addition, isoform 1, but not isoform 2, binds ADP-ribose and O-acetyl-ADP-ribose, and may be involved in ADP-ribose-mediated chromatin modulation.1 Publication

    GO - Molecular functioni

    1. chromatin binding Source: Ensembl
    2. DNA binding Source: UniProtKB-KW

    GO - Biological processi

    1. chromatin modification Source: UniProtKB-KW
    2. dosage compensation Source: Ensembl
    3. nucleosome assembly Source: InterPro

    Keywords - Molecular functioni

    Chromatin regulator

    Keywords - Ligandi

    DNA-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Core histone macro-H2A.1
    Short name:
    Histone macroH2A1
    Short name:
    mH2A1
    Alternative name(s):
    H2A.y
    H2A/y
    Gene namesi
    Name:H2afy
    OrganismiRattus norvegicus (Rat)
    Taxonomic identifieri10116 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
    ProteomesiUP000002494: Chromosome 17

    Organism-specific databases

    RGDi621462. H2afy.

    Subcellular locationi

    Nucleus By similarity. Chromosome By similarity
    Note: Enriched in inactive X chromosome chromatin and in senescence-associated heterochromatin.By similarity

    GO - Cellular componenti

    1. Barr body Source: Ensembl
    2. condensed chromosome Source: Ensembl
    3. nucleosome Source: RGD

    Keywords - Cellular componenti

    Chromosome, Nucleosome core, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 371371Core histone macro-H2A.1PRO_0000055319Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei18 – 181N6-methyllysineBy similarity
    Modified residuei116 – 1161N6-acetyllysine; alternateBy similarity
    Cross-linki116 – 116Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternateBy similarity
    Cross-linki117 – 117Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
    Modified residuei123 – 1231N6-acetyllysineBy similarity
    Modified residuei129 – 1291PhosphothreonineBy similarity
    Modified residuei169 – 1691PhosphoserineBy similarity
    Modified residuei172 – 1721PhosphoserineBy similarity

    Post-translational modificationi

    Monoubiquitinated at either Lys-116 or Lys-117. May also be polyubiquitinated. Ubiquitination is mediated by the CUL3/SPOP E3 complex and does not promote proteasomal degradation. Instead, it is required for enrichment in inactive X chromosome chromatin By similarity.By similarity

    Keywords - PTMi

    Acetylation, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

    Proteomic databases

    PaxDbiQ02874.
    PRIDEiQ02874.

    PTM databases

    PhosphoSiteiQ02874.

    Expressioni

    Tissue specificityi

    Isoform 1 is present only in liver and brain, whereas isoform 2 is present in brain, thymus, testis, liver and kidney (at protein level).1 Publication

    Gene expression databases

    ArrayExpressiQ02874.
    GenevestigatoriQ02874.

    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. Interacts with SPOP. Part of a complex consisting of H2AFY, CUL3 and SPOP. Interacts with HDAC1 and HDAC2 By similarity.By similarity

    Protein-protein interaction databases

    STRINGi10116.ENSRNOP00000049143.

    Structurei

    Secondary structure

    1
    371
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi229 – 25123
    Beta strandi259 – 2635
    Beta strandi267 – 2759
    Helixi285 – 30218
    Beta strandi306 – 3105
    Beta strandi314 – 3163
    Helixi322 – 33716
    Beta strandi347 – 3515
    Helixi355 – 36511
    Turni366 – 3694

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1YD9X-ray1.60A/B/C/D229-371[»]
    ProteinModelPortaliQ02874.
    SMRiQ02874. Positions 10-117, 180-368.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ02874.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini2 – 117116Histone H2AAdd
    BLAST
    Domaini183 – 369187MacroPROSITE-ProRule annotationAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi118 – 16144Lys-richAdd
    BLAST

    Sequence similaritiesi

    Contains 1 histone H2A domain.Curated
    Contains 1 Macro domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG2110.
    GeneTreeiENSGT00740000115227.
    HOGENOMiHOG000234653.
    HOVERGENiHBG009342.
    InParanoidiQ02874.
    KOiK11251.
    OMAiQVVQADI.
    OrthoDBiEOG71G9VP.
    PhylomeDBiQ02874.

    Family and domain databases

    Gene3Di1.10.20.10. 1 hit.
    InterProiIPR021171. Core_histone_macro-H2A.
    IPR009072. Histone-fold.
    IPR007125. Histone_core_D.
    IPR002119. Histone_H2A.
    IPR002589. Macro_dom.
    [Graphical view]
    PfamiPF00125. Histone. 1 hit.
    PF01661. Macro. 1 hit.
    [Graphical view]
    PIRSFiPIRSF037942. Core_histone_macro-H2A. 1 hit.
    PRINTSiPR00620. HISTONEH2A.
    SMARTiSM00506. A1pp. 1 hit.
    SM00414. H2A. 1 hit.
    [Graphical view]
    SUPFAMiSSF47113. SSF47113. 1 hit.
    PROSITEiPS51154. MACRO. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 2 (identifier: Q02874-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MSSRGGKKKS TKTSRSAKAG VIFPVGRMLR YIKKGHPKYR IGVGAPVYMA    50
    AVLEYLTAEI LELAGNAARD NKKGRVTPRH ILLAVANDEE LNQLLKGVTI 100
    ASGGVLPNIH PELLAKKRGS KGKLEAIITP PPAKKAKSPS QKKPVAKKTG 150
    GKKGARKSKK QGEVSKAASA DSTTEGAPTD GFTVLSTKSL FLGQKLNLIH 200
    SEISNLAGFE VEAIINPTNA DIDLKDDLGS TLEKKGGKEF VEAVLELRKK 250
    NGPLEVAGAA VSAGHGLPAK FVIHCNSPVW GADKCEELLE KTVKNCLALA 300
    DDRKLKSIAF PSIGSGRNGF PKQTAAQLIL KAISSYFVST MSSSIKTVYF 350
    VLFDSESIGI YVQEMAKLDA N 371
    Length:371
    Mass (Da):39,504
    Last modified:January 23, 2007 - v4
    Checksum:i697D4EF813AAAC6D
    GO
    Isoform 1 (identifier: Q02874-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         197-228: NLIHSEISNLAGFEVEAIINPTNADIDLKDDL → QVVQADIASIDSDAVVHPTNADFYIGGEV

    Show »
    Length:368
    Mass (Da):39,040
    Checksum:i59ACA1B086CF5C69
    GO

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei197 – 22832NLIHS…LKDDL → QVVQADIASIDSDAVVHPTN ADFYIGGEV in isoform 1. 1 PublicationVSP_002057Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M99065 mRNA. Translation: AAA41561.2.
    M99066 mRNA. Translation: AAA41560.1.
    U79139 mRNA. Translation: AAB38330.1.
    BC089093 mRNA. Translation: AAH89093.1.
    PIRiI59567.
    I80811.
    RefSeqiNP_058878.1. NM_017182.2. [Q02874-1]
    XP_006253638.1. XM_006253576.1.
    UniGeneiRn.11098.

    Genome annotation databases

    EnsembliENSRNOT00000015632; ENSRNOP00000015632; ENSRNOG00000011523.
    ENSRNOT00000051702; ENSRNOP00000049143; ENSRNOG00000011523. [Q02874-1]
    GeneIDi29384.
    KEGGirno:29384.
    UCSCiRGD:621462. rat. [Q02874-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M99065 mRNA. Translation: AAA41561.2 .
    M99066 mRNA. Translation: AAA41560.1 .
    U79139 mRNA. Translation: AAB38330.1 .
    BC089093 mRNA. Translation: AAH89093.1 .
    PIRi I59567.
    I80811.
    RefSeqi NP_058878.1. NM_017182.2. [Q02874-1 ]
    XP_006253638.1. XM_006253576.1.
    UniGenei Rn.11098.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1YD9 X-ray 1.60 A/B/C/D 229-371 [» ]
    ProteinModelPortali Q02874.
    SMRi Q02874. Positions 10-117, 180-368.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 10116.ENSRNOP00000049143.

    PTM databases

    PhosphoSitei Q02874.

    Proteomic databases

    PaxDbi Q02874.
    PRIDEi Q02874.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSRNOT00000015632 ; ENSRNOP00000015632 ; ENSRNOG00000011523 .
    ENSRNOT00000051702 ; ENSRNOP00000049143 ; ENSRNOG00000011523 . [Q02874-1 ]
    GeneIDi 29384.
    KEGGi rno:29384.
    UCSCi RGD:621462. rat. [Q02874-1 ]

    Organism-specific databases

    CTDi 9555.
    RGDi 621462. H2afy.

    Phylogenomic databases

    eggNOGi COG2110.
    GeneTreei ENSGT00740000115227.
    HOGENOMi HOG000234653.
    HOVERGENi HBG009342.
    InParanoidi Q02874.
    KOi K11251.
    OMAi QVVQADI.
    OrthoDBi EOG71G9VP.
    PhylomeDBi Q02874.

    Miscellaneous databases

    EvolutionaryTracei Q02874.
    NextBioi 608979.

    Gene expression databases

    ArrayExpressi Q02874.
    Genevestigatori Q02874.

    Family and domain databases

    Gene3Di 1.10.20.10. 1 hit.
    InterProi IPR021171. Core_histone_macro-H2A.
    IPR009072. Histone-fold.
    IPR007125. Histone_core_D.
    IPR002119. Histone_H2A.
    IPR002589. Macro_dom.
    [Graphical view ]
    Pfami PF00125. Histone. 1 hit.
    PF01661. Macro. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF037942. Core_histone_macro-H2A. 1 hit.
    PRINTSi PR00620. HISTONEH2A.
    SMARTi SM00506. A1pp. 1 hit.
    SM00414. H2A. 1 hit.
    [Graphical view ]
    SUPFAMi SSF47113. SSF47113. 1 hit.
    PROSITEi PS51154. MACRO. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "MacroH2A, a core histone containing a large nonhistone region."
      Pehrson J.R., Fried V.A.
      Science 257:1398-1400(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), PARTIAL PROTEIN SEQUENCE.
      Tissue: Liver.
    2. Pehrson J.R.
      Submitted (FEB-2006) to the EMBL/GenBank/DDBJ databases
      Cited for: SEQUENCE REVISION (ISOFORM 1).
    3. "Developmental and tissue expression patterns of histone macroH2A1 subtypes."
      Pehrson J.R., Costanzi C., Dharia C.
      J. Cell. Biochem. 65:107-113(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), TISSUE SPECIFICITY.
      Tissue: Thymus.
    4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
      Strain: Brown Norway.
      Tissue: Kidney.
    5. Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 181-371 (ISOFORM 1), FUNCTION.

    Entry informationi

    Entry nameiH2AY_RAT
    AccessioniPrimary (citable) accession number: Q02874
    Secondary accession number(s): O09140, Q63325
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1994
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 124 of the entry and version 4 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