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P04912

- H2A2_YEAST

UniProt

P04912 - H2A2_YEAST

Protein

Histone H2A.2

Gene

HTA2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
  1. Functioni

    Core component of nucleosome which plays a central role in DNA double strand break (DSB) repair. 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.4 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei120 – 1201Not ubiquitinatedCurated

    GO - Molecular functioni

    1. DNA binding Source: SGD

    GO - Biological processi

    1. chromatin assembly or disassembly Source: SGD
    2. DNA repair Source: SGD
    3. nucleosome assembly Source: InterPro

    Keywords - Biological processi

    DNA damage, DNA repair

    Keywords - Ligandi

    DNA-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-28909-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Histone H2A.2
    Gene namesi
    Name:HTA2
    Synonyms:H2A2
    Ordered Locus Names:YBL003C
    ORF Names:YBL0103
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome II

    Organism-specific databases

    SGDiS000000099. HTA2.

    Subcellular locationi

    GO - Cellular componenti

    1. nuclear nucleosome Source: SGD
    2. replication fork protection complex Source: SGD

    Keywords - Cellular componenti

    Chromosome, Nucleosome core, Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi129 – 1291S → A: Causes hypersensitivity to DNA-damage-inducing agents. 1 Publication
    Mutagenesisi129 – 1291S → E or T: No effect. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 132131Histone H2A.2PRO_0000055327Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylserine1 Publication
    Modified residuei5 – 51N6-acetyllysine1 Publication
    Modified residuei8 – 81N6-acetyllysine2 Publications
    Modified residuei106 – 1061N5-methylglutamine1 Publication
    Cross-linki127 – 127Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)
    Modified residuei129 – 1291Phosphoserine2 Publications

    Post-translational modificationi

    Phosphorylated to form H2AS128ph (gamma-H2A) in response to DNA double-strand breaks (DSBs) generated by exogenous genotoxic agents and by stalled replication forks. Phosphorylation is dependent on the DNA damage checkpoint kinases MEC1/ATR and TEL1/ATM, spreads on either side of a detected DSB site and may mark the surrounding chromatin for recruitment of proteins required for DNA damage signaling and repair. Gamma-H2A interacts with ARP4, a shared component of the NuA4 histone acetyltransferase complex and the INO80 and SWR1 chromatin remodeling complexes, and serves to recruit first NuA4, mediating histone H4 acetylation, and subsequently the INO80/SWR1 complexes, facilitating DNA resection, to DSB sites. Gamma-H2A is required for sequestering cohesin around the break site, which is important for efficient post-replicative double-strand break repair by homologous recombination, holding the damaged chromatid close to its undamaged sister template. Gamma-H2A is removed from the DNA prior to the strand invasion-primer extension step of the repair process and subsequently dephosphorylated by PPH3, a component of the histone H2A phosphatase complex (HTP-C). Dephosphorylation is necessary for efficient recovery from the DNA damage checkpoint.4 Publications
    N-acetylated by NAT4.
    Acetylated by ESA1, a component of the NuA4 histone acetyltransferase (HAT) complex, to form H2AK4ac and H2AK7ac.
    Glutamine methylation at Gln-106 (H2AQ105me) by NOP1 is specifically dedicated to polymerase I. It is present at 35S ribosomal DNA locus and impairs binding of the FACT complex (PubMed:24352239).1 Publication
    Sumoylated to from H2AK126su. May lead to transcriptional repression.1 Publication

    Keywords - PTMi

    Acetylation, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

    Proteomic databases

    MaxQBiP04912.
    PaxDbiP04912.

    Expressioni

    Gene expression databases

    GenevestigatoriP04912.

    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 NAP1.2 Publications

    Protein-protein interaction databases

    BioGridi32699. 282 interactions.
    DIPiDIP-6377N.
    IntActiP04912. 156 interactions.
    MINTiMINT-637879.
    STRINGi4932.YBL003C.

    Structurei

    Secondary structure

    1
    132
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi19 – 224
    Helixi29 – 379
    Turni38 – 403
    Beta strandi43 – 453
    Helixi49 – 7426
    Beta strandi78 – 803
    Helixi82 – 898
    Helixi93 – 986
    Turni99 – 1013
    Beta strandi102 – 1043
    Helixi115 – 1173

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4JJNX-ray3.09C/G2-132[»]
    4KUDX-ray3.20C/G1-132[»]
    ProteinModelPortaliP04912.
    SMRiP04912. Positions 17-122.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi129 – 1302[ST]-Q motif

    Domaini

    The [ST]-Q motif constitutes a recognition sequence for kinases from the PI3/PI4-kinase family.

    Sequence similaritiesi

    Belongs to the histone H2A family.Curated

    Phylogenomic databases

    eggNOGiCOG5262.
    GeneTreeiENSGT00740000115227.
    HOGENOMiHOG000234652.
    KOiK11251.
    OMAiTKNAQSR.
    OrthoDBiEOG7GN30N.

    Family and domain databases

    Gene3Di1.10.20.10. 1 hit.
    InterProiIPR009072. Histone-fold.
    IPR007125. Histone_core_D.
    IPR002119. Histone_H2A.
    [Graphical view]
    PfamiPF00125. Histone. 1 hit.
    [Graphical view]
    PRINTSiPR00620. HISTONEH2A.
    SMARTiSM00414. H2A. 1 hit.
    [Graphical view]
    SUPFAMiSSF47113. SSF47113. 1 hit.
    PROSITEiPS00046. HISTONE_H2A. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P04912-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSGGKGGKAG SAAKASQSRS AKAGLTFPVG RVHRLLRRGN YAQRIGSGAP    50
    VYLTAVLEYL AAEILELAGN AARDNKKTRI IPRHLQLAIR NDDELNKLLG 100
    NVTIAQGGVL PNIHQNLLPK KSAKTAKASQ EL 132
    Length:132
    Mass (Da):13,989
    Last modified:January 23, 2007 - v2
    Checksum:iE808C94A0363CD53
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    V01305 Genomic DNA. Translation: CAA24612.1.
    Z26494 Genomic DNA. Translation: CAA81267.1.
    Z35764 Genomic DNA. Translation: CAA84818.1.
    AY693115 Genomic DNA. Translation: AAT93134.1.
    BK006936 Genomic DNA. Translation: DAA07119.1.
    PIRiS05814. HSBYA2.
    RefSeqiNP_009552.1. NM_001178243.1.

    Genome annotation databases

    EnsemblFungiiYBL003C; YBL003C; YBL003C.
    GeneIDi852283.
    KEGGisce:YBL003C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    V01305 Genomic DNA. Translation: CAA24612.1 .
    Z26494 Genomic DNA. Translation: CAA81267.1 .
    Z35764 Genomic DNA. Translation: CAA84818.1 .
    AY693115 Genomic DNA. Translation: AAT93134.1 .
    BK006936 Genomic DNA. Translation: DAA07119.1 .
    PIRi S05814. HSBYA2.
    RefSeqi NP_009552.1. NM_001178243.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4JJN X-ray 3.09 C/G 2-132 [» ]
    4KUD X-ray 3.20 C/G 1-132 [» ]
    ProteinModelPortali P04912.
    SMRi P04912. Positions 17-122.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 32699. 282 interactions.
    DIPi DIP-6377N.
    IntActi P04912. 156 interactions.
    MINTi MINT-637879.
    STRINGi 4932.YBL003C.

    Proteomic databases

    MaxQBi P04912.
    PaxDbi P04912.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YBL003C ; YBL003C ; YBL003C .
    GeneIDi 852283.
    KEGGi sce:YBL003C.

    Organism-specific databases

    SGDi S000000099. HTA2.

    Phylogenomic databases

    eggNOGi COG5262.
    GeneTreei ENSGT00740000115227.
    HOGENOMi HOG000234652.
    KOi K11251.
    OMAi TKNAQSR.
    OrthoDBi EOG7GN30N.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-28909-MONOMER.

    Miscellaneous databases

    NextBioi 970913.
    PROi P04912.

    Gene expression databases

    Genevestigatori P04912.

    Family and domain databases

    Gene3Di 1.10.20.10. 1 hit.
    InterProi IPR009072. Histone-fold.
    IPR007125. Histone_core_D.
    IPR002119. Histone_H2A.
    [Graphical view ]
    Pfami PF00125. Histone. 1 hit.
    [Graphical view ]
    PRINTSi PR00620. HISTONEH2A.
    SMARTi SM00414. H2A. 1 hit.
    [Graphical view ]
    SUPFAMi SSF47113. SSF47113. 1 hit.
    PROSITEi PS00046. HISTONE_H2A. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The two yeast histone H2A genes encode similar protein subtypes."
      Choe J., Kolodrubetz D., Grunstein M.
      Proc. Natl. Acad. Sci. U.S.A. 79:1484-1487(1982) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Sequence around the centromere of Saccharomyces cerevisiae chromosome II: similarity of CEN2 to CEN4."
      Wolfe K.H., Lohan A.J.E.
      Yeast 10:S41-S46(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. "Complete DNA sequence of yeast chromosome II."
      Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C.
      , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K.
      EMBO J. 13:5795-5809(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    4. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    5. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    6. "Esa1p is an essential histone acetyltransferase required for cell cycle progression."
      Clarke A.S., Lowell J.E., Jacobson S.J., Pillus L.
      Mol. Cell. Biol. 19:2515-2526(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION AT LYS-5 AND LYS-8.
    7. "A role for Saccharomyces cerevisiae histone H2A in DNA repair."
      Downs J.A., Lowndes N.F., Jackson S.P.
      Nature 408:1001-1004(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, MUTAGENESIS OF SER-129, PHOSPHORYLATION AT SER-129.
    8. "Highly specific antibodies determine histone acetylation site usage in yeast heterochromatin and euchromatin."
      Suka N., Suka Y., Carmen A.A., Wu J., Grunstein M.
      Mol. Cell 8:473-479(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION AT LYS-8.
    9. "An Nalpha-acetyltransferase responsible for acetylation of the N-terminal residues of histones H4 and H2A."
      Song O.-K., Wang X., Waterborg J.H., Sternglanz R.
      J. Biol. Chem. 278:38109-38112(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION AT SER-2.
    10. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    11. "Distribution and dynamics of chromatin modification induced by a defined DNA double-strand break."
      Shroff R., Arbel-Eden A., Pilch D.R., Ira G., Bonner W.M., Petrini J.H.J., Haber J.E., Lichten M.
      Curr. Biol. 14:1703-1711(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, PHOSPHORYLATION.
    12. "DNA damage response pathway uses histone modification to assemble a double-strand break-specific cohesin domain."
      Uenal E., Arbel-Eden A., Sattler U., Shroff R., Lichten M., Haber J.E., Koshland D.
      Mol. Cell 16:991-1002(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, PHOSPHORYLATION.
    13. "Binding of chromatin-modifying activities to phosphorylated histone H2A at DNA damage sites."
      Downs J.A., Allard S., Jobin-Robitaille O., Javaheri A., Auger A., Bouchard N., Kron S.J., Jackson S.P., Cote J.
      Mol. Cell 16:979-990(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH ARP4.
    14. "Histone sumoylation is a negative regulator in Saccharomyces cerevisiae and shows dynamic interplay with positive-acting histone modifications."
      Nathan D., Ingvarsdottir K., Sterner D.E., Bylebyl G.R., Dokmanovic M., Dorsey J.A., Whelan K.A., Krsmanovic M., Lane W.S., Meluh P.B., Johnson E.S., Berger S.L.
      Genes Dev. 20:966-976(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUMOYLATION AT LYS-127.
    15. Cited for: FUNCTION, DEPHOSPHORYLATION.
    16. "Phosphorylation by casein kinase 2 regulates Nap1 localization and function."
      Calvert M.E.K., Keck K.M., Ptak C., Shabanowitz J., Hunt D.F., Pemberton L.F.
      Mol. Cell. Biol. 28:1313-1325(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH NAP1, IDENTIFICATION BY MASS SPECTROMETRY.
    17. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
      Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
      Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-129, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    18. "Glutamine methylation in histone H2A is an RNA-polymerase-I-dedicated modification."
      Tessarz P., Santos-Rosa H., Robson S.C., Sylvestersen K.B., Nelson C.J., Nielsen M.L., Kouzarides T.
      Nature 505:564-568(2014) [PubMed] [Europe PMC] [Abstract]
      Cited for: METHYLATION AT GLN-106.

    Entry informationi

    Entry nameiH2A2_YEAST
    AccessioniPrimary (citable) accession number: P04912
    Secondary accession number(s): D6VPZ9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 13, 1987
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 140 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    In contrast to vertebrates and insects, its C-terminus is not monoubiquitinated.Curated
    Present with 32100 molecules/cell in log phase SD medium.1 Publication

    Caution

    To ensure consistency between histone entries, we follow the 'Brno' nomenclature for histone modifications, with positions referring to those used in the literature for the 'closest' model organism. Due to slight variations in histone sequences between organisms and to the presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the actual positions of modified amino acids in the sequence generally differ. In this entry the following conventions are used: H2AK4ac = acetylated Lys-5; H2AK7ac = acetylated Lys-8; H2AK126su = sumoylated Lys-127; H2AS128ph = phosphorylated Ser-129.Curated

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
    3. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome II
      Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names

    External Data

    Dasty 3