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P04911

- H2A1_YEAST

UniProt

P04911 - H2A1_YEAST

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Protein

Histone H2A.1

Gene

HTA1

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

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 ubiquitinated

GO - Molecular functioni

  1. DNA binding Source: SGD

GO - Biological processi

  1. chromatin assembly or disassembly Source: SGD
  2. DNA repair Source: SGD
  3. negative regulation of transcription from RNA polymerase II promoter Source: SGD
  4. transfer RNA gene-mediated silencing Source: SGD
Complete GO annotation...

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-29805-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H2A.1
Gene namesi
Name:HTA1
Synonyms:H2A1, SPT11
Ordered Locus Names:YDR225W
ORF Names:YD9934.10
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome IV

Organism-specific databases

SGDiS000002633. HTA1.

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi120 – 1212KK → RR: No effect. No effect; when associated with R-124 and R-127. 2 Publications
Mutagenesisi122 – 1221S → A or E: Causes hypersensitivity to DNA-damage-inducing agents and impairs sporulation. 1 Publication
Mutagenesisi124 – 1241K → R: No effect; when associated with R-120; R-121 and R-127. 1 Publication
Mutagenesisi127 – 1271K → R: No effect; when associated with R-120; R-121 and R-124. 1 Publication
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.1PRO_0000055326Add
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 – 1291Phosphoserine1 Publication

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.3 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

Expressioni

Gene expression databases

GenevestigatoriP04911.

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.

Protein-protein interaction databases

BioGridi32277. 410 interactions.
DIPiDIP-419N.
IntActiP04911. 22 interactions.
MINTiMINT-398033.
STRINGi4932.YDR225W.

Structurei

Secondary structure

1
132
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi21 – 233Combined sources
Helixi29 – 379Combined sources
Beta strandi43 – 453Combined sources
Helixi49 – 7426Combined sources
Beta strandi78 – 803Combined sources
Helixi82 – 909Combined sources
Helixi93 – 986Combined sources
Turni99 – 1013Combined sources
Beta strandi102 – 1043Combined sources
Helixi115 – 1173Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ID3X-ray3.10C/G2-132[»]
3T7KX-ray2.03C/D125-132[»]
ProteinModelPortaliP04911.
SMRiP04911. Positions 17-122.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04911.

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

GeneTreeiENSGT00760000119217.
HOGENOMiHOG000234652.
InParanoidiP04911.
KOiK11251.
OMAiGYKRAGP.
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.

P04911-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSGGKGGKAG SAAKASQSRS AKAGLTFPVG RVHRLLRRGN YAQRIGSGAP
60 70 80 90 100
VYLTAVLEYL AAEILELAGN AARDNKKTRI IPRHLQLAIR NDDELNKLLG
110 120 130
NVTIAQGGVL PNIHQNLLPK KSAKATKASQ EL
Length:132
Mass (Da):13,989
Last modified:January 23, 2007 - v2
Checksum:iA908C94A0363D13F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
V01304 Genomic DNA. Translation: CAA24611.1.
U13239 Genomic DNA. Translation: AAC33142.1.
Z48612 Genomic DNA. Translation: CAA88505.1.
M18455 Genomic DNA. Translation: AAA66318.1.
BK006938 Genomic DNA. Translation: DAA12067.1.
PIRiS05813. HSBYA1.
RefSeqiNP_010511.3. NM_001180533.3.

Genome annotation databases

EnsemblFungiiYDR225W; YDR225W; YDR225W.
GeneIDi851811.
KEGGisce:YDR225W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
V01304 Genomic DNA. Translation: CAA24611.1 .
U13239 Genomic DNA. Translation: AAC33142.1 .
Z48612 Genomic DNA. Translation: CAA88505.1 .
M18455 Genomic DNA. Translation: AAA66318.1 .
BK006938 Genomic DNA. Translation: DAA12067.1 .
PIRi S05813. HSBYA1.
RefSeqi NP_010511.3. NM_001180533.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1ID3 X-ray 3.10 C/G 2-132 [» ]
3T7K X-ray 2.03 C/D 125-132 [» ]
ProteinModelPortali P04911.
SMRi P04911. Positions 17-122.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 32277. 410 interactions.
DIPi DIP-419N.
IntActi P04911. 22 interactions.
MINTi MINT-398033.
STRINGi 4932.YDR225W.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YDR225W ; YDR225W ; YDR225W .
GeneIDi 851811.
KEGGi sce:YDR225W.

Organism-specific databases

SGDi S000002633. HTA1.

Phylogenomic databases

GeneTreei ENSGT00760000119217.
HOGENOMi HOG000234652.
InParanoidi P04911.
KOi K11251.
OMAi GYKRAGP.
OrthoDBi EOG7GN30N.

Enzyme and pathway databases

BioCyci YEAST:G3O-29805-MONOMER.

Miscellaneous databases

EvolutionaryTracei P04911.
NextBioi 969665.

Gene expression databases

Genevestigatori P04911.

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

« Hide 'large scale' publications
  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. "Insertion site specificity of the transposon Tn3."
    Davies C.J., Hutchison C.A. III
    Nucleic Acids Res. 23:507-514(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
    Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
    , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
    Nature 387:75-78(1997) [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. "Analysis and in vivo disruption of the gene coding for adenylate kinase (ADK1) in the yeast Saccharomyces cerevisiae."
    Konrad M.
    J. Biol. Chem. 263:19468-19474(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 15-132.
  6. "A conserved sequence in histone H2A which is a ubiquitination site in higher eucaryotes is not required for growth in Saccharomyces cerevisiae."
    Swerdlow P.S., Schuster T., Finley D.
    Mol. Cell. Biol. 10:4905-4911(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: LACK OF UBIQUITINATION, MUTAGENESIS OF 120-LYS-LYS-121.
  7. "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.
  8. "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.
  9. "Rad6-dependent ubiquitination of histone H2B in yeast."
    Robzyk K., Recht J., Osley M.A.
    Science 287:501-504(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: LACK OF UBIQUITINATION, MUTAGENESIS OF 120-LYS-LYS-121; LYS-124 AND LYS-127.
  10. "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.
  11. "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.
  12. "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.
  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. "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.
  15. "Saccharomyces cerevisiae histone H2A Ser122 facilitates DNA repair."
    Harvey A.C., Jackson S.P., Downs J.A.
    Genetics 170:543-553(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF SER-122.
  16. "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.
  17. Cited for: FUNCTION, DEPHOSPHORYLATION.
  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.
  19. "Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions."
    White C.L., Suto R.K., Luger K.
    EMBO J. 20:5207-5218(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS).

Entry informationi

Entry nameiH2A1_YEAST
AccessioniPrimary (citable) accession number: P04911
Secondary accession number(s): D6VSK7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: January 23, 2007
Last modified: November 26, 2014
This is version 154 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.

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 IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

External Data

Dasty 3