H2AXB_ARATH
ID H2AXB_ARATH Reviewed; 142 AA.
AC Q9S9K7;
DT 07-FEB-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 147.
DE RecName: Full=Probable histone H2AXb;
DE AltName: Full=HTA3;
GN OrderedLocusNames=At1g54690; ORFNames=T22H22.12;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP PHOSPHORYLATION.
RX PubMed=15772150; DOI=10.1091/mbc.e04-10-0890;
RA Friesner J.D., Liu B., Culligan K., Britt A.B.;
RT "Ionizing radiation-dependent gamma-H2AX focus formation requires ataxia
RT telangiectasia mutated and ataxia telangiectasia mutated and Rad3-
RT related.";
RL Mol. Biol. Cell 16:2566-2576(2005).
RN [6]
RP TISSUE SPECIFICITY, AND NOMENCLATURE.
RX PubMed=16751347; DOI=10.1105/tpc.105.039719;
RA Yi H., Sardesai N., Fujinuma T., Chan C.-W., Veena X., Gelvin S.B.;
RT "Constitutive expression exposes functional redundancy between the
RT Arabidopsis histone H2A gene HTA1 and other H2A gene family members.";
RL Plant Cell 18:1575-1589(2006).
CC -!- FUNCTION: Variant histone H2A which replaces conventional H2A in a
CC subset of nucleosomes. Nucleosomes wrap and compact DNA into chromatin,
CC limiting DNA accessibility to the cellular machineries which require
CC DNA as a template. Histones thereby play a central role in
CC transcription regulation, DNA repair, DNA replication and chromosomal
CC stability. DNA accessibility is regulated via a complex set of post-
CC translational modifications of histones, also called histone code, and
CC nucleosome remodeling. Required for checkpoint-mediated arrest of cell
CC cycle progression in response to low doses of ionizing radiation and
CC for efficient repair of DNA double strand breaks (DSBs) specifically
CC when modified by C-terminal phosphorylation (By similarity).
CC {ECO:0000250}.
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 numerous proteins required for DNA damage signaling
CC and repair when phosphorylated on Ser-139 (By similarity).
CC {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}. Chromosome {ECO:0000250}.
CC -!- TISSUE SPECIFICITY: Expressed in meristems and dividing cells.
CC {ECO:0000269|PubMed:16751347}.
CC -!- DOMAIN: The [ST]-Q motif constitutes a recognition sequence for kinases
CC from the PI3/PI4-kinase family.
CC -!- PTM: Phosphorylated to form H2AXS139ph (gamma-H2AX) in response to DNA
CC double strand breaks (DSBs) generated by exogenous genotoxic agents and
CC by stalled replication forks, and may also occur during meiotic
CC recombination events. Phosphorylation can extend up to several thousand
CC nucleosomes from the actual site of the DSB and may mark the
CC surrounding chromatin for recruitment of proteins required for DNA
CC damage signaling and repair. Widespread phosphorylation may also serve
CC to amplify the damage signal or aid repair of persistent lesions.
CC H2AXS139ph in response to ionizing radiation is mediated by ATM while
CC defects in DNA replication induce H2AXS139ph subsequent to activation
CC of ATR. Dephosphorylation of H2AXS139ph by PP2A is required for DNA DSB
CC repair (By similarity). {ECO:0000250}.
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: H2AXS139ph =
CC phosphorylated Ser-139. {ECO:0000305}.
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DR EMBL; AC005388; AAC64883.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE33135.1; -; Genomic_DNA.
DR EMBL; AY094023; AAM16179.1; -; mRNA.
DR EMBL; AF411788; AAL06478.1; -; mRNA.
DR EMBL; AY085671; AAM62890.1; -; mRNA.
DR PIR; A96589; A96589.
DR RefSeq; NP_175868.1; NM_104344.2.
DR AlphaFoldDB; Q9S9K7; -.
DR SMR; Q9S9K7; -.
DR BioGRID; 27135; 1.
DR IntAct; Q9S9K7; 1.
DR STRING; 3702.AT1G54690.1; -.
DR iPTMnet; Q9S9K7; -.
DR PaxDb; Q9S9K7; -.
DR PRIDE; Q9S9K7; -.
DR ProteomicsDB; 247348; -.
DR EnsemblPlants; AT1G54690.1; AT1G54690.1; AT1G54690.
DR GeneID; 841910; -.
DR Gramene; AT1G54690.1; AT1G54690.1; AT1G54690.
DR KEGG; ath:AT1G54690; -.
DR Araport; AT1G54690; -.
DR TAIR; locus:2199486; AT1G54690.
DR eggNOG; KOG1756; Eukaryota.
DR HOGENOM; CLU_062828_3_0_1; -.
DR InParanoid; Q9S9K7; -.
DR OMA; VMPYIHP; -.
DR OrthoDB; 1504122at2759; -.
DR PhylomeDB; Q9S9K7; -.
DR PRO; PR:Q9S9K7; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9S9K7; baseline and differential.
DR Genevisible; Q9S9K7; AT.
DR GO; GO:0005730; C:nucleolus; HDA:TAIR.
DR GO; GO:0000786; C:nucleosome; IEA:UniProtKB-KW.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
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 CDD; cd00074; H2A; 1.
DR Gene3D; 1.10.20.10; -; 1.
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 Chromosome; DNA-binding; Nucleosome core; Nucleus; Phosphoprotein;
KW Reference proteome.
FT CHAIN 1..142
FT /note="Probable histone H2AXb"
FT /id="PRO_0000055199"
FT REGION 1..28
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 139..140
FT /note="[ST]-Q motif"
FT MOD_RES 139
FT /note="Phosphoserine; by ATM and ATR"
FT /evidence="ECO:0000305"
SQ SEQUENCE 142 AA; 14783 MW; 1593C683FCF7E680 CRC64;
MSSGAGSGTT KGGRGKPKAT KSVSRSSKAG LQFPVGRIAR FLKAGKYAER VGAGAPVYLS
AVLEYLAAEV LELAGNAARD NKKTRIVPRH IQLAVRNDEE LSKLLGSVTI ANGGVLPNIH
QTLLPSKVGK NKGDIGSASQ EF
