P04911 (H2A1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Histone H2A.1

Gene names

Name:	HTA1
Synonyms:	H2A1, SPT11
Ordered Locus Names:	YDR225W
ORF Names:	YD9934.10

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.8 Ref.13 Ref.15 Ref.18
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.
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.8 Ref.13 Ref.15 Ref.18 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.17
Miscellaneous	In contrast to vertebrates and insects, its C-terminus is not monoubiquitinated.
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	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA repair Inferred from mutant phenotype Ref.16. Source: SGD chromatin assembly or disassembly Traceable author statement PubMed 2275823. Source: SGD negative regulation of transcription from RNA polymerase II promoter Inferred from mutant phenotype PubMed 17526727. 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.1

PRO_0000055326

Regions

Motif

129 – 130

2

[ST]-Q motif

Sites

Site

120

1

Not ubiquitinated

Amino acid modifications

Modified residue

2

1

N-acetylserine Ref.12

Modified residue

5

1

N6-acetyllysine Ref.7

Modified residue

8

1

N6-acetyllysine Ref.7 Ref.10

Modified residue

129

1

Phosphoserine Ref.8 Ref.11

Cross-link

127

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Ref.17

Experimental info

Mutagenesis

120 – 121

2

KK → RR: No effect. No effect; when associated with R-124 and R-127. Ref.6

Mutagenesis

122

1

S → A or E: Causes hypersensitivity to DNA-damage-inducing agents and impairs sporulation. Ref.6 Ref.16

Mutagenesis

124

1

K → R: No effect; when associated with R-120; R-121 and R-127. Ref.6 Ref.9

Mutagenesis

127

1

K → R: No effect; when associated with R-120; R-121 and R-124. Ref.6 Ref.9

Mutagenesis

129

1

S → A: Causes hypersensitivity to DNA-damage-inducing agents. Ref.6 Ref.8

Mutagenesis

129

1

S → E or T: No effect. Ref.6 Ref.8

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

132

Helix Strand Turn

Details...

Helix

21 – 23

3

Helix

29 – 37

9

Beta strand

43 – 45

3

Helix

49 – 74

26

Beta strand

78 – 80

3

Helix

82 – 90

9

Helix

93 – 98

6

Turn

99 – 101

3

Beta strand

102 – 104

3

Helix

115 – 117

3

Sequences

	Sequence		Length	Mass (Da)
	P04911 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: A908C94A0363D13F	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 KSAKATKASQ 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]	"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 204511 / S288c / AB972.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases 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]	"Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae." Ficarro S.B., McCleland M.L., Stukenberg P.T., Burke D.J., Ross M.M., Shabanowitz J., Hunt D.F., White F.M. Nat. Biotechnol. 20:301-305(2002) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-129, MASS SPECTROMETRY. Strain: 2124.
[12]	"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.
[13]	"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.
[14]	"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.
[15]	"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.
[16]	"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.
[17]	"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.
[18]	"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.
[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).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

PIR

HSBYA1. S05813.

RefSeq

NP_010511.3. NM_001180533.3.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P04911.

SMR

P04911. Positions 17-126.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-419N.

IntAct

P04911. 35 interactions.

MINT

MINT-398033.

STRING

4932.YDR225W.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YDR225W; YDR225W; YDR225W.

GeneID

851811.

KEGG

sce:YDR225W.
sce:YDR229W.

Organism-specific databases

SGD

S000002633. HTA1.

Phylogenomic databases

GeneTree

ENSGT00690000101783.

HOGENOM

HOG000234652.

KO

K11251.

OMA

ICNDEEL.

OrthoDB

EOG4GQTFP.

Gene expression databases

Genevestigator

P04911.

GermOnline

YDR225W. 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

EvolutionaryTrace

P04911.

NextBio

969665.

Entry information

Entry name

H2A1_YEAST

Accession

Primary (citable) accession number: P04911
Secondary accession number(s): D6VSK7

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 13, 1987
Last sequence update:	January 23, 2007
Last modified:	April 3, 2013
This is version 141 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program