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P04912 (H2A2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 138. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Histone H2A.2
Gene names
Name:HTA2
Synonyms:H2A2
Ordered Locus Names:YBL003C
ORF Names:YBL0103
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length132 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.7 Ref.11 Ref.12 Ref.15

Subunit structure

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. Ref.13 Ref.16

Subcellular location

Nucleus. Chromosome.

Domain

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

Post-translational modification

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. Ref.7 Ref.11 Ref.12 Ref.15

N-acetylated by NAT4. Ref.6 Ref.8 Ref.9

Acetylated by ESA1, a component of the NuA4 histone acetyltransferase (HAT) complex, to form H2AK4ac and H2AK7ac. Ref.6 Ref.8 Ref.9

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 (Ref.18).

Sumoylated to from H2AK126su. May lead to transcriptional repression. Ref.14

Miscellaneous

In contrast to vertebrates and insects, its C-terminus is not monoubiquitinated Probable.

Present with 32100 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the histone H2A family.

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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed
Chain2 – 132131Histone H2A.2
PRO_0000055327

Regions

Motif129 – 1302[ST]-Q motif

Sites

Site1201Not ubiquitinated Probable

Amino acid modifications

Modified residue21N-acetylserine Ref.9
Modified residue51N6-acetyllysine Ref.6
Modified residue81N6-acetyllysine Ref.6 Ref.8
Modified residue1061N5-methylglutamine Ref.18
Modified residue1291Phosphoserine Ref.7 Ref.17
Cross-link127Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Ref.14

Experimental info

Mutagenesis1291S → A: Causes hypersensitivity to DNA-damage-inducing agents. Ref.7
Mutagenesis1291S → E or T: No effect. Ref.7

Secondary structure

.................... 132
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P04912 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: E808C94A0363CD53

FASTA13213,989
        10         20         30         40         50         60 
MSGGKGGKAG SAAKASQSRS AKAGLTFPVG RVHRLLRRGN YAQRIGSGAP VYLTAVLEYL 

        70         80         90        100        110        120 
AAEILELAGN AARDNKKTRI IPRHLQLAIR NDDELNKLLG NVTIAQGGVL PNIHQNLLPK 

       130 
KSAKTAKASQ EL 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[5]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
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]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
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]"A phosphatase complex that dephosphorylates gamma-H2AX regulates DNA damage checkpoint recovery."
Keogh M.-C., Kim J.-A., Downey M., Fillingham J., Chowdhury D., Harrison J.C., Onishi M., Datta N., Galicia S., Emili A., Lieberman J., Shen X., Buratowski S., Haber J.E., Durocher D., Greenblatt J.F., Krogan N.J.
Nature 439:497-501(2006) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRHSBYA2. S05814.
RefSeqNP_009552.1. NM_001178243.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4JJNX-ray3.09C/G2-132[»]
4KUDX-ray3.20C/G1-132[»]
ProteinModelPortalP04912.
SMRP04912. Positions 17-122.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid32699. 282 interactions.
DIPDIP-6377N.
IntActP04912. 156 interactions.
MINTMINT-637879.
STRING4932.YBL003C.

Proteomic databases

PaxDbP04912.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYBL003C; YBL003C; YBL003C.
GeneID852283.
KEGGsce:YBL003C.

Organism-specific databases

SGDS000000099. HTA2.

Phylogenomic databases

eggNOGCOG5262.
GeneTreeENSGT00740000115227.
HOGENOMHOG000234652.
KOK11251.
OMATKNAQSR.
OrthoDBEOG7GN30N.

Enzyme and pathway databases

BioCycYEAST:G3O-28909-MONOMER.

Gene expression databases

GenevestigatorP04912.

Family and domain databases

Gene3D1.10.20.10. 1 hit.
InterProIPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR002119. Histone_H2A.
[Graphical view]
PfamPF00125. Histone. 1 hit.
[Graphical view]
PRINTSPR00620. HISTONEH2A.
SMARTSM00414. H2A. 1 hit.
[Graphical view]
SUPFAMSSF47113. SSF47113. 1 hit.
PROSITEPS00046. HISTONE_H2A. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio970913.
PROP04912.

Entry information

Entry nameH2A2_YEAST
AccessionPrimary (citable) accession number: P04912
Secondary accession number(s): D6VPZ9
Entry history
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: January 23, 2007
Last modified: April 16, 2014
This is version 138 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome II

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

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references