P04912 (H2A2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Histone H2A.2

Gene names

Name:	HTA2
Synonyms:	H2A2
Ordered Locus Names:	YBL003C
ORF Names:	YBL0103

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	132 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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. Acetylated by ESA1, a component of the NuA4 histone acetyltransferase (HAT) complex, to form H2AK4ac and H2AK7ac. 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.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Cellular component	Chromosome Nucleosome core Nucleus
Ligand	DNA-binding
PTM	Acetylation Isopeptide bond Phosphoprotein Ubl conjugation
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA repair Inferred from mutant phenotype PubMed 15781691. Source: SGD chromatin assembly or disassembly Traceable author statement PubMed 2275823. Source: SGD nucleosome assembly Inferred from electronic annotation. Source: InterPro
Cellular_component	nuclear nucleosome Traceable author statement PubMed 2275823. Source: SGD replication fork protection complex Inferred from direct assay PubMed 16531994. Source: SGD
Molecular_function	DNA binding Traceable author statement PubMed 2275823. Source: SGD
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Initiator methionine	1	1	Removed
	Chain	2 – 132	131	Histone H2A.2		PRO_0000055327
Regions
	Motif	129 – 130	2	[ST]-Q motif
Sites
	Site	120	1	Not ubiquitinated Probable
Amino acid modifications
	Modified residue	2	1	N-acetylserine Ref.9
	Modified residue	5	1	N6-acetyllysine Ref.6
	Modified residue	8	1	N6-acetyllysine Ref.6 Ref.8
	Modified residue	129	1	Phosphoserine Ref.7 Ref.17
	Cross-link	127		Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Ref.14
Experimental info
	Mutagenesis	129	1	S → A: Causes hypersensitivity to DNA-damage-inducing agents. Ref.7
	Mutagenesis	129	1	S → E or T: No effect. Ref.7

Sequences

	Sequence		Length	Mass (Da)
	P04912 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: E808C94A0363CD53	FASTA	132	13,989
	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

References

	« Hide 'large scale' referencesShow '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. , 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. , 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, 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, MASS SPECTROMETRY.
+	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.
PIR	HSBYA2. S05814.
RefSeq	NP_009552.1. NM_001178243.1.
3D structure databases
ProteinModelPortal	P04912.
SMR	P04912. Positions 14-121.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-6377N.
IntAct	P04912. 159 interactions.
MINT	MINT-637879.
STRING	4932.YBL003C.
Proteomic databases
PaxDb	P04912.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YBL003C; YBL003C; YBL003C.
GeneID	852283.
KEGG	sce:YBL003C.
Organism-specific databases
SGD	S000000099. HTA2.
Phylogenomic databases
eggNOG	COG5262.
GeneTree	ENSGT00690000101783.
HOGENOM	HOG000234652.
KO	K11251.
OMA	HINWSIN.
OrthoDB	EOG4GQTFP.
Enzyme and pathway databases
BioCyc	YEAST:G3O-28909-MONOMER.
Gene expression databases
Genevestigator	P04912.
GermOnline	YBL003C. Saccharomyces cerevisiae.
Family and domain databases
Gene3D	1.10.20.10. 1 hit.
InterPro	IPR009072. Histone-fold. IPR007125. Histone_core_D. IPR002119. Histone_H2A. [Graphical view]
Pfam	PF00125. Histone. 1 hit. [Graphical view]
PRINTS	PR00620. HISTONEH2A.
SMART	SM00414. H2A. 1 hit. [Graphical view]
SUPFAM	SSF47113. Histone-fold. 1 hit.
PROSITE	PS00046. HISTONE_H2A. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	970913.

Entry information

Entry name

H2A2_YEAST

Accession

Primary (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:	May 29, 2013
This is version 130 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program