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Protein

Histone H2A.2

Gene

HTA2

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

Miscellaneous

In contrast to vertebrates and insects, its C-terminus is not monoubiquitinated.Curated
Present with 32100 molecules/cell in log phase SD medium.1 Publication

GO - Molecular functioni

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

GO - Biological processi

  • chromatin assembly or disassembly Source: SGD
  • chromatin silencing Source: GO_Central
  • DNA repair Source: SGD

Keywordsi

Molecular functionDNA-binding
Biological processDNA damage, DNA repair

Enzyme and pathway databases

BioCyciYEAST:G3O-28909-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-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-8936459. RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H2A.2
Gene namesi
Name:HTA2
Synonyms:H2A2
Ordered Locus Names:YBL003C
ORF Names:YBL0103
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome II

Organism-specific databases

EuPathDBiFungiDB:YBL003C.
SGDiS000000099. HTA2.

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
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_00000553272 – 132Histone H2A.2Add BLAST131

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserine1 Publication1
Modified residuei5N6-acetyllysine1 Publication1
Modified residuei8N6-acetyllysine2 Publications1
Modified residuei106N5-methylglutamine1 Publication1
Cross-linki127Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)
Modified residuei129PhosphoserineCombined sources1 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 ubiquitinatedCurated1

Keywords - PTMi

Acetylation, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP04912.
PRIDEiP04912.
TopDownProteomicsiP04912.

PTM databases

iPTMnetiP04912.

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. Interacts with NAP1.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
ABF2Q024866EBI-8076,EBI-2028
ASE1P502752EBI-8076,EBI-2045397
CKA1P157905EBI-8076,EBI-9533
CKA2P194544EBI-8076,EBI-9548
DBF4P323252EBI-8076,EBI-5575
EAF5P399952EBI-8076,EBI-22312
EAF6P471283EBI-8076,EBI-25552
ENP1P383332EBI-8076,EBI-6482
EPL1P435724EBI-8076,EBI-22792
ERP2P397042EBI-8076,EBI-6587
ESA1Q086494EBI-8076,EBI-6648
GAL11P196592EBI-8076,EBI-7305
GPD2P419114EBI-8076,EBI-7791
HAT1Q1234112EBI-8076,EBI-8176
HCA4P204488EBI-8076,EBI-5612
HHF2P0230916EBI-8076,EBI-8113
HHT2P6183027EBI-8076,EBI-8098
HMO1Q039734EBI-8076,EBI-33047
HTA1P049113EBI-8076,EBI-8072
HTB1P022936EBI-8076,EBI-8088
HTB2P0229417EBI-8076,EBI-8094
IES1P435792EBI-8076,EBI-22775
IOC4Q042132EBI-8076,EBI-28077
KAP114P5306741EBI-8076,EBI-9174
KAR2P164744EBI-8076,EBI-7876
NAP1P2529334EBI-8076,EBI-11850
NHP2P324953EBI-8076,EBI-12014
NOP1P156462EBI-8076,EBI-6838
NSE4P431244EBI-8076,EBI-14410
NUP188P525934EBI-8076,EBI-11763
ORC2P328332EBI-8076,EBI-12572
ORC6P388263EBI-8076,EBI-12588
OSH2Q1245112EBI-8076,EBI-12621
PMT1P337752EBI-8076,EBI-13567
POB3Q0463616EBI-8076,EBI-27863
PPH3P323455EBI-8076,EBI-12759
PSY2P401648EBI-8076,EBI-29107
PSY4P381933EBI-8076,EBI-21239
REB1P215382EBI-8076,EBI-14905
RFC1P386304EBI-8076,EBI-14985
RFC3P386293EBI-8076,EBI-15000
RIM1P324452EBI-8076,EBI-15206
RSC58Q079797EBI-8076,EBI-36549
RTG2P326082EBI-8076,EBI-16322
SAS3P342184EBI-8076,EBI-16484
SCC4P400903EBI-8076,EBI-16679
SDO1Q079532EBI-8076,EBI-27124
SEC28P405092EBI-8076,EBI-4884
SGV1P232932EBI-8076,EBI-17078
SPC1P469652EBI-8076,EBI-17823
SPT16P3255842EBI-8076,EBI-4334
SSB2P401504EBI-8076,EBI-8632
SVL3Q030883EBI-8076,EBI-36005
SWC7Q067072EBI-8076,EBI-32671
TIF2P100812EBI-8076,EBI-9017
TOP2P067867EBI-8076,EBI-19352
UBP8P501024EBI-8076,EBI-19863
UME6P390012EBI-8076,EBI-20086
VTH1P404384EBI-8076,EBI-3662633
YKU70P328072EBI-8076,EBI-8214
YNG2P388063EBI-8076,EBI-24622

GO - Molecular functioni

Protein-protein interaction databases

BioGridi32699. 307 interactors.
DIPiDIP-6377N.
IntActiP04912. 245 interactors.
MINTiMINT-637879.
STRINGi4932.YBL003C.

Structurei

Secondary structure

1132
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi19 – 22Combined sources4
Helixi29 – 37Combined sources9
Turni38 – 40Combined sources3
Beta strandi43 – 45Combined sources3
Helixi49 – 74Combined sources26
Beta strandi78 – 80Combined sources3
Helixi82 – 89Combined sources8
Helixi93 – 98Combined sources6
Turni99 – 101Combined sources3
Beta strandi102 – 104Combined sources3
Helixi115 – 117Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4JJNX-ray3.09C/G2-132[»]
4KUDX-ray3.20C/G1-132[»]
ProteinModelPortaliP04912.
SMRiP04912.
ModBaseiSearch...
MobiDBiSearch...

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

GeneTreeiENSGT00880000137879.
HOGENOMiHOG000234652.
InParanoidiP04912.
KOiK11251.
OMAiFANVTIR.
OrthoDBiEOG092C5QJX.

Family and domain databases

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.

P04912-1 [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 KSAKTAKASQ EL
Length:132
Mass (Da):13,989
Last modified:January 23, 2007 - v2
Checksum:iE808C94A0363CD53
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiS05814. HSBYA2.
RefSeqiNP_009552.1. NM_001178243.1.

Genome annotation databases

EnsemblFungiiYBL003C; YBL003C; YBL003C.
GeneIDi852283.
KEGGisce:YBL003C.

Similar proteinsi

Entry informationi

Entry nameiH2A2_YEAST
AccessioniPrimary (citable) accession number: P04912
Secondary accession number(s): D6VPZ9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: January 23, 2007
Last modified: September 27, 2017
This is version 167 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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