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Protein

Histone H2A.1

Gene

HTA1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: -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

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

GO - Molecular functioni

  • DNA binding Source: SGD
  • protein heterodimerization activity Source: InterPro

GO - Biological processi

  • chromatin assembly or disassembly Source: SGD
  • DNA repair Source: SGD
  • negative regulation of transcription by RNA polymerase II Source: SGD
  • transfer RNA gene-mediated silencing Source: SGD

Keywordsi

Molecular functionDNA-binding
Biological processDNA damage, DNA repair

Enzyme and pathway databases

BioCyciYEAST:G3O-29805-MONOMER
ReactomeiR-SCE-2299718 Condensation of Prophase Chromosomes
R-SCE-2559580 Oxidative Stress Induced Senescence
R-SCE-2559582 Senescence-Associated Secretory Phenotype (SASP)
R-SCE-3214815 HDACs deacetylate histones
R-SCE-3214847 HATs acetylate histones
R-SCE-3214858 RMTs methylate histone arginines
R-SCE-427359 SIRT1 negatively regulates rRNA expression
R-SCE-5625886 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
R-SCE-5689880 Ub-specific processing proteases
R-SCE-5689901 Metalloprotease DUBs
R-SCE-5693565 Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
R-SCE-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
R-SCE-9018519 Estrogen-dependent gene expression

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
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDR225W
SGDiS000002633 HTA1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi120 – 121KK → RR: No effect. No effect; when associated with R-124 and R-127. 2 Publications2
Mutagenesisi122S → A or E: Causes hypersensitivity to DNA-damage-inducing agents and impairs sporulation. 1 Publication1
Mutagenesisi124K → R: No effect; when associated with R-120; R-121 and R-127. 1 Publication1
Mutagenesisi127K → R: No effect; when associated with R-120; R-121 and R-124. 1 Publication1
Mutagenesisi129S → A: Causes hypersensitivity to DNA-damage-inducing agents. 1 Publication1
Mutagenesisi129S → E or T: No effect. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00000553262 – 132Histone H2A.1Add BLAST131

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserine1 Publication1
Modified residuei5N6-acetyllysine1 Publication1
Modified residuei8N6-acetyllysine2 Publications1
Modified residuei14N6-succinyllysine1 Publication1
Modified residuei22N6-succinyllysine1 Publication1
Modified residuei106N5-methylglutamine1 Publication1
Modified residuei120N6-malonyllysine; alternate1 Publication1
Cross-linki127Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)
Modified residuei129Phosphoserine1 Publication1

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei120Not ubiquitinated2 Publications1

Keywords - PTMi

Acetylation, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP04911
PaxDbiP04911
PRIDEiP04911

PTM databases

iPTMnetiP04911

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.

Binary interactionsi

WithEntry#Exp.IntActNotes
NAP1P252933EBI-8072,EBI-11850

GO - Molecular functioni

Protein-protein interaction databases

BioGridi32277, 602 interactors
ComplexPortaliCPX-1612 Nucleosome, variant HTA1-HTB1
CPX-2566 Nucleosome, variant HTA1-HTB2
DIPiDIP-419N
ELMiP04911
IntActiP04911, 53 interactors
MINTiP04911
STRINGi4932.YDR225W

Structurei

Secondary structure

1132
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi19 – 23Combined sources5
Helixi29 – 38Combined sources10
Beta strandi41 – 45Combined sources5
Helixi48 – 74Combined sources27
Beta strandi78 – 80Combined sources3
Helixi82 – 90Combined sources9
Helixi93 – 99Combined sources7
Beta strandi102 – 104Combined sources3
Helixi115 – 117Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1ID3X-ray3.10C/G2-132[»]
3T7KX-ray2.03C/D125-132[»]
4WNNX-ray1.80A/C/E/G1-132[»]
5BT1X-ray2.62C1-132[»]
ProteinModelPortaliP04911
SMRiP04911
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04911

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi129 – 130[ST]-Q motif2

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

GeneTreeiENSGT00910000143981
HOGENOMiHOG000234652
InParanoidiP04911
KOiK11251
OMAiGKEGHEP
OrthoDBiEOG092C5QJX

Family and domain databases

CDDicd00074 H2A, 1 hit
Gene3Di1.10.20.10, 1 hit
InterProiView protein in InterPro
IPR009072 Histone-fold
IPR002119 Histone_H2A
IPR007125 Histone_H2A/H2B/H3
IPR032454 Histone_H2A_C
IPR032458 Histone_H2A_CS
PfamiView protein in Pfam
PF00125 Histone, 1 hit
PF16211 Histone_H2A_C, 1 hit
PRINTSiPR00620 HISTONEH2A
SMARTiView protein in SMART
SM00414 H2A, 1 hit
SUPFAMiSSF47113 SSF47113, 1 hit
PROSITEiView protein in PROSITE
PS00046 HISTONE_H2A, 1 hit

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

Similar proteinsi

Entry informationi

Entry nameiH2A1_YEAST
AccessioniPrimary (citable) accession number: P04911
Secondary accession number(s): D6VSK7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: January 23, 2007
Last modified: June 20, 2018
This is version 190 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

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