H2A2_YEAST
ID H2A2_YEAST Reviewed; 132 AA.
AC P04912; D6VPZ9;
DT 13-AUG-1987, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 199.
DE RecName: Full=Histone H2A.2;
GN Name=HTA2; Synonyms=H2A2; OrderedLocusNames=YBL003C; ORFNames=YBL0103;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=7041122; DOI=10.1073/pnas.79.5.1484;
RA Choe J., Kolodrubetz D., Grunstein M.;
RT "The two yeast histone H2A genes encode similar protein subtypes.";
RL Proc. Natl. Acad. Sci. U.S.A. 79:1484-1487(1982).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8091860; DOI=10.1002/yea.320100006;
RA Wolfe K.H., Lohan A.J.E.;
RT "Sequence around the centromere of Saccharomyces cerevisiae chromosome II:
RT similarity of CEN2 to CEN4.";
RL Yeast 10:S41-S46(1994).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7813418; DOI=10.1002/j.1460-2075.1994.tb06923.x;
RA Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C.,
RA Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M.,
RA Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M.,
RA Cziepluch C., Demolis N., Delaveau T., Doignon F., Domdey H.,
RA Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D.,
RA Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N.,
RA Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J.,
RA Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C.,
RA Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P.,
RA Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y.,
RA Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F.,
RA Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E.,
RA Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M.,
RA Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B.,
RA Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L.,
RA Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M.,
RA Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S.,
RA Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K.,
RA Mewes H.-W., Kleine K.;
RT "Complete DNA sequence of yeast chromosome II.";
RL EMBO J. 13:5795-5809(1994).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [6]
RP ACETYLATION AT LYS-5 AND LYS-8.
RX PubMed=10082517; DOI=10.1128/mcb.19.4.2515;
RA Clarke A.S., Lowell J.E., Jacobson S.J., Pillus L.;
RT "Esa1p is an essential histone acetyltransferase required for cell cycle
RT progression.";
RL Mol. Cell. Biol. 19:2515-2526(1999).
RN [7]
RP FUNCTION, MUTAGENESIS OF SER-129, AND PHOSPHORYLATION AT SER-129.
RX PubMed=11140636; DOI=10.1038/35050000;
RA Downs J.A., Lowndes N.F., Jackson S.P.;
RT "A role for Saccharomyces cerevisiae histone H2A in DNA repair.";
RL Nature 408:1001-1004(2000).
RN [8]
RP ACETYLATION AT LYS-8.
RX PubMed=11545749; DOI=10.1016/s1097-2765(01)00301-x;
RA Suka N., Suka Y., Carmen A.A., Wu J., Grunstein M.;
RT "Highly specific antibodies determine histone acetylation site usage in
RT yeast heterochromatin and euchromatin.";
RL Mol. Cell 8:473-479(2001).
RN [9]
RP ACETYLATION AT SER-2.
RX PubMed=12915400; DOI=10.1074/jbc.c300355200;
RA Song O.-K., Wang X., Waterborg J.H., Sternglanz R.;
RT "An Nalpha-acetyltransferase responsible for acetylation of the N-terminal
RT residues of histones H4 and H2A.";
RL J. Biol. Chem. 278:38109-38112(2003).
RN [10]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [11]
RP FUNCTION, AND PHOSPHORYLATION.
RX PubMed=15458641; DOI=10.1016/j.cub.2004.09.047;
RA Shroff R., Arbel-Eden A., Pilch D.R., Ira G., Bonner W.M., Petrini J.H.J.,
RA Haber J.E., Lichten M.;
RT "Distribution and dynamics of chromatin modification induced by a defined
RT DNA double-strand break.";
RL Curr. Biol. 14:1703-1711(2004).
RN [12]
RP FUNCTION, AND PHOSPHORYLATION.
RX PubMed=15610741; DOI=10.1016/j.molcel.2004.11.027;
RA Uenal E., Arbel-Eden A., Sattler U., Shroff R., Lichten M., Haber J.E.,
RA Koshland D.;
RT "DNA damage response pathway uses histone modification to assemble a
RT double-strand break-specific cohesin domain.";
RL Mol. Cell 16:991-1002(2004).
RN [13]
RP INTERACTION WITH ARP4.
RX PubMed=15610740; DOI=10.1016/j.molcel.2004.12.003;
RA Downs J.A., Allard S., Jobin-Robitaille O., Javaheri A., Auger A.,
RA Bouchard N., Kron S.J., Jackson S.P., Cote J.;
RT "Binding of chromatin-modifying activities to phosphorylated histone H2A at
RT DNA damage sites.";
RL Mol. Cell 16:979-990(2004).
RN [14]
RP SUMOYLATION AT LYS-127.
RX PubMed=16598039; DOI=10.1101/gad.1404206;
RA Nathan D., Ingvarsdottir K., Sterner D.E., Bylebyl G.R., Dokmanovic M.,
RA Dorsey J.A., Whelan K.A., Krsmanovic M., Lane W.S., Meluh P.B.,
RA Johnson E.S., Berger S.L.;
RT "Histone sumoylation is a negative regulator in Saccharomyces cerevisiae
RT and shows dynamic interplay with positive-acting histone modifications.";
RL Genes Dev. 20:966-976(2006).
RN [15]
RP FUNCTION, AND DEPHOSPHORYLATION.
RX PubMed=16299494; DOI=10.1038/nature04384;
RA Keogh M.-C., Kim J.-A., Downey M., Fillingham J., Chowdhury D.,
RA Harrison J.C., Onishi M., Datta N., Galicia S., Emili A., Lieberman J.,
RA Shen X., Buratowski S., Haber J.E., Durocher D., Greenblatt J.F.,
RA Krogan N.J.;
RT "A phosphatase complex that dephosphorylates gamma-H2AX regulates DNA
RT damage checkpoint recovery.";
RL Nature 439:497-501(2006).
RN [16]
RP INTERACTION WITH NAP1, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=18086883; DOI=10.1128/mcb.01035-07;
RA Calvert M.E.K., Keck K.M., Ptak C., Shabanowitz J., Hunt D.F.,
RA Pemberton L.F.;
RT "Phosphorylation by casein kinase 2 regulates Nap1 localization and
RT function.";
RL Mol. Cell. Biol. 28:1313-1325(2008).
RN [17]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-129, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [18]
RP SUCCINYLATION AT LYS-14 AND LYS-22, AND MALONYLATION AT LYS-120.
RX PubMed=22389435; DOI=10.1074/mcp.m111.015875;
RA Xie Z., Dai J., Dai L., Tan M., Cheng Z., Wu Y., Boeke J.D., Zhao Y.;
RT "Lysine succinylation and lysine malonylation in histones.";
RL Mol. Cell. Proteomics 11:100-107(2012).
RN [19]
RP METHYLATION AT GLN-106.
RX PubMed=24352239; DOI=10.1038/nature12819;
RA Tessarz P., Santos-Rosa H., Robson S.C., Sylvestersen K.B., Nelson C.J.,
RA Nielsen M.L., Kouzarides T.;
RT "Glutamine methylation in histone H2A is an RNA-polymerase-I-dedicated
RT modification.";
RL Nature 505:564-568(2014).
CC -!- FUNCTION: Core component of nucleosome which plays a central role in
CC DNA double strand break (DSB) repair. Nucleosomes wrap and compact DNA
CC into chromatin, limiting DNA accessibility to the cellular machineries
CC which require DNA as a template. Histones thereby play a central role
CC in transcription regulation, DNA repair, DNA replication and
CC chromosomal stability. DNA accessibility is regulated via a complex set
CC of post-translational modifications of histones, also called histone
CC code, and nucleosome remodeling. {ECO:0000269|PubMed:11140636,
CC ECO:0000269|PubMed:15458641, ECO:0000269|PubMed:15610741,
CC ECO:0000269|PubMed:16299494}.
CC -!- SUBUNIT: The nucleosome is a histone octamer containing two molecules
CC each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and
CC two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of
CC DNA. Interacts with NAP1. {ECO:0000269|PubMed:15610740,
CC ECO:0000269|PubMed:18086883}.
CC -!- SUBCELLULAR LOCATION: Nucleus. Chromosome.
CC -!- DOMAIN: The [ST]-Q motif constitutes a recognition sequence for kinases
CC from the PI3/PI4-kinase family.
CC -!- PTM: Phosphorylated to form H2AS128ph (gamma-H2A) in response to DNA
CC double-strand breaks (DSBs) generated by exogenous genotoxic agents and
CC by stalled replication forks. Phosphorylation is dependent on the DNA
CC damage checkpoint kinases MEC1/ATR and TEL1/ATM, spreads on either side
CC of a detected DSB site and may mark the surrounding chromatin for
CC recruitment of proteins required for DNA damage signaling and repair.
CC Gamma-H2A interacts with ARP4, a shared component of the NuA4 histone
CC acetyltransferase complex and the INO80 and SWR1 chromatin remodeling
CC complexes, and serves to recruit first NuA4, mediating histone H4
CC acetylation, and subsequently the INO80/SWR1 complexes, facilitating
CC DNA resection, to DSB sites. Gamma-H2A is required for sequestering
CC cohesin around the break site, which is important for efficient post-
CC replicative double-strand break repair by homologous recombination,
CC holding the damaged chromatid close to its undamaged sister template.
CC Gamma-H2A is removed from the DNA prior to the strand invasion-primer
CC extension step of the repair process and subsequently dephosphorylated
CC by PPH3, a component of the histone H2A phosphatase complex (HTP-C).
CC Dephosphorylation is necessary for efficient recovery from the DNA
CC damage checkpoint. {ECO:0000269|PubMed:11140636,
CC ECO:0000269|PubMed:15458641, ECO:0000269|PubMed:15610741}.
CC -!- PTM: N-acetylated by NAT4.
CC -!- PTM: Acetylated by ESA1, a component of the NuA4 histone
CC acetyltransferase (HAT) complex, to form H2AK4ac and H2AK7ac.
CC -!- PTM: Glutamine methylation at Gln-106 (H2AQ105me) by NOP1 is
CC specifically dedicated to polymerase I. It is present at 35S ribosomal
CC DNA locus and impairs binding of the FACT complex (PubMed:24352239).
CC {ECO:0000269|PubMed:24352239}.
CC -!- PTM: Sumoylated to from H2AK126su. May lead to transcriptional
CC repression. {ECO:0000269|PubMed:16598039}.
CC -!- MISCELLANEOUS: In contrast to vertebrates and insects, its C-terminus
CC is not monoubiquitinated. {ECO:0000305}.
CC -!- MISCELLANEOUS: Present with 32100 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the histone H2A family. {ECO:0000305}.
CC -!- CAUTION: To ensure consistency between histone entries, we follow the
CC 'Brno' nomenclature for histone modifications, with positions referring
CC to those used in the literature for the 'closest' model organism. Due
CC to slight variations in histone sequences between organisms and to the
CC presence of initiator methionine in UniProtKB/Swiss-Prot sequences, the
CC actual positions of modified amino acids in the sequence generally
CC differ. In this entry the following conventions are used: H2AK4ac =
CC acetylated Lys-5; H2AK7ac = acetylated Lys-8; H2AK126su = sumoylated
CC Lys-127; H2AS128ph = phosphorylated Ser-129. {ECO:0000305}.
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DR EMBL; V01305; CAA24612.1; -; Genomic_DNA.
DR EMBL; Z26494; CAA81267.1; -; Genomic_DNA.
DR EMBL; Z35764; CAA84818.1; -; Genomic_DNA.
DR EMBL; AY693115; AAT93134.1; -; Genomic_DNA.
DR EMBL; BK006936; DAA07119.1; -; Genomic_DNA.
DR PIR; S05814; HSBYA2.
DR RefSeq; NP_009552.1; NM_001178243.1.
DR PDB; 4JJN; X-ray; 3.09 A; C/G=2-132.
DR PDB; 4KUD; X-ray; 3.20 A; C/G=1-132.
DR PDBsum; 4JJN; -.
DR PDBsum; 4KUD; -.
DR AlphaFoldDB; P04912; -.
DR SMR; P04912; -.
DR BioGRID; 32699; 320.
DR ComplexPortal; CPX-1610; Nucleosome, variant HTA2-HTB2.
DR ComplexPortal; CPX-1611; Nucleosome, variant HTA2-HTB1.
DR DIP; DIP-6377N; -.
DR IntAct; P04912; 162.
DR MINT; P04912; -.
DR STRING; 4932.YBL003C; -.
DR iPTMnet; P04912; -.
DR MaxQB; P04912; -.
DR PaxDb; P04912; -.
DR PRIDE; P04912; -.
DR TopDownProteomics; P04912; -.
DR EnsemblFungi; YBL003C_mRNA; YBL003C; YBL003C.
DR GeneID; 852283; -.
DR KEGG; sce:YBL003C; -.
DR SGD; S000000099; HTA2.
DR VEuPathDB; FungiDB:YBL003C; -.
DR eggNOG; KOG1756; Eukaryota.
DR GeneTree; ENSGT00940000153118; -.
DR HOGENOM; CLU_062828_3_0_1; -.
DR InParanoid; P04912; -.
DR OMA; VMPYIHP; -.
DR BioCyc; YEAST:G3O-28909-MON; -.
DR Reactome; R-SCE-2299718; Condensation of Prophase Chromosomes.
DR Reactome; R-SCE-2559580; Oxidative Stress Induced Senescence.
DR Reactome; R-SCE-3214815; HDACs deacetylate histones.
DR Reactome; R-SCE-3214858; RMTs methylate histone arginines.
DR Reactome; R-SCE-427359; SIRT1 negatively regulates rRNA expression.
DR Reactome; R-SCE-5625886; Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3.
DR Reactome; R-SCE-5689880; Ub-specific processing proteases.
DR Reactome; R-SCE-5693565; Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
DR Reactome; R-SCE-68616; Assembly of the ORC complex at the origin of replication.
DR Reactome; R-SCE-73772; RNA Polymerase I Promoter Escape.
DR Reactome; R-SCE-9018519; Estrogen-dependent gene expression.
DR PRO; PR:P04912; -.
DR Proteomes; UP000002311; Chromosome II.
DR RNAct; P04912; protein.
DR GO; GO:0000786; C:nucleosome; TAS:SGD.
DR GO; GO:0005634; C:nucleus; IC:ComplexPortal.
DR GO; GO:0031298; C:replication fork protection complex; IDA:SGD.
DR GO; GO:0003677; F:DNA binding; IBA:GO_Central.
DR GO; GO:0046982; F:protein heterodimerization activity; IEA:InterPro.
DR GO; GO:0030527; F:structural constituent of chromatin; IEA:InterPro.
DR GO; GO:0006325; P:chromatin organization; TAS:SGD.
DR GO; GO:0006281; P:DNA repair; IMP:SGD.
DR CDD; cd00074; H2A; 1.
DR Gene3D; 1.10.20.10; -; 1.
DR IDEAL; IID50137; -.
DR InterPro; IPR009072; Histone-fold.
DR InterPro; IPR002119; Histone_H2A.
DR InterPro; IPR007125; Histone_H2A/H2B/H3.
DR InterPro; IPR032454; Histone_H2A_C.
DR InterPro; IPR032458; Histone_H2A_CS.
DR PANTHER; PTHR23430; PTHR23430; 1.
DR Pfam; PF00125; Histone; 1.
DR Pfam; PF16211; Histone_H2A_C; 1.
DR PRINTS; PR00620; HISTONEH2A.
DR SMART; SM00414; H2A; 1.
DR SUPFAM; SSF47113; SSF47113; 1.
DR PROSITE; PS00046; HISTONE_H2A; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Chromosome; DNA damage; DNA repair; DNA-binding;
KW Isopeptide bond; Methylation; Nucleosome core; Nucleus; Phosphoprotein;
KW Reference proteome; Ubl conjugation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:12915400"
FT CHAIN 2..132
FT /note="Histone H2A.2"
FT /id="PRO_0000055327"
FT MOTIF 129..130
FT /note="[ST]-Q motif"
FT SITE 120
FT /note="Not ubiquitinated"
FT /evidence="ECO:0000305"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0000269|PubMed:12915400"
FT MOD_RES 5
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000269|PubMed:10082517"
FT MOD_RES 8
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000269|PubMed:10082517,
FT ECO:0000269|PubMed:11545749"
FT MOD_RES 14
FT /note="N6-succinyllysine"
FT /evidence="ECO:0000269|PubMed:22389435"
FT MOD_RES 22
FT /note="N6-succinyllysine"
FT /evidence="ECO:0000269|PubMed:22389435"
FT MOD_RES 106
FT /note="N5-methylglutamine"
FT /evidence="ECO:0000269|PubMed:24352239"
FT MOD_RES 120
FT /note="N6-malonyllysine"
FT /evidence="ECO:0000269|PubMed:22389435"
FT MOD_RES 129
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:11140636,
FT ECO:0007744|PubMed:18407956"
FT CROSSLNK 127
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO)"
FT MUTAGEN 129
FT /note="S->A: Causes hypersensitivity to DNA-damage-inducing
FT agents."
FT /evidence="ECO:0000269|PubMed:11140636"
FT MUTAGEN 129
FT /note="S->E,T: No effect."
FT /evidence="ECO:0000269|PubMed:11140636"
FT HELIX 19..22
FT /evidence="ECO:0007829|PDB:4JJN"
FT HELIX 29..37
FT /evidence="ECO:0007829|PDB:4JJN"
FT TURN 38..40
FT /evidence="ECO:0007829|PDB:4JJN"
FT STRAND 43..45
FT /evidence="ECO:0007829|PDB:4JJN"
FT HELIX 49..74
FT /evidence="ECO:0007829|PDB:4JJN"
FT STRAND 78..80
FT /evidence="ECO:0007829|PDB:4JJN"
FT HELIX 82..89
FT /evidence="ECO:0007829|PDB:4JJN"
FT HELIX 93..98
FT /evidence="ECO:0007829|PDB:4JJN"
FT TURN 99..101
FT /evidence="ECO:0007829|PDB:4JJN"
FT STRAND 102..104
FT /evidence="ECO:0007829|PDB:4JJN"
FT HELIX 115..117
FT /evidence="ECO:0007829|PDB:4JJN"
SQ SEQUENCE 132 AA; 13989 MW; E808C94A0363CD53 CRC64;
MSGGKGGKAG SAAKASQSRS AKAGLTFPVG RVHRLLRRGN YAQRIGSGAP VYLTAVLEYL
AAEILELAGN AARDNKKTRI IPRHLQLAIR NDDELNKLLG NVTIAQGGVL PNIHQNLLPK
KSAKTAKASQ EL
