H2AXB_ORYSJ
ID H2AXB_ORYSJ Reviewed; 138 AA.
AC Q2QPG9; B7F7P0; Q0IMX6;
DT 13-JUN-2006, integrated into UniProtKB/Swiss-Prot.
DT 24-JAN-2006, sequence version 1.
DT 03-AUG-2022, entry version 97.
DE RecName: Full=Probable histone H2AXb;
GN OrderedLocusNames=Os12g0530000, LOC_Os12g34510;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16188032; DOI=10.1186/1741-7007-3-20;
RG The rice chromosomes 11 and 12 sequencing consortia;
RT "The sequence of rice chromosomes 11 and 12, rich in disease resistance
RT genes and recent gene duplications.";
RL BMC Biol. 3:20-20(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
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-135 (By similarity).
CC {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}. Chromosome {ECO:0000250}.
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-135. {ECO:0000305}.
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DR EMBL; DP000011; ABA98778.1; -; Genomic_DNA.
DR EMBL; AP008218; BAF29939.1; -; Genomic_DNA.
DR EMBL; AP014968; BAT17434.1; -; Genomic_DNA.
DR EMBL; AK121752; BAH00638.1; -; mRNA.
DR RefSeq; XP_015618536.1; XM_015763050.1.
DR AlphaFoldDB; Q2QPG9; -.
DR SMR; Q2QPG9; -.
DR STRING; 4530.OS12T0530000-01; -.
DR PaxDb; Q2QPG9; -.
DR PRIDE; Q2QPG9; -.
DR EnsemblPlants; Os12t0530000-01; Os12t0530000-01; Os12g0530000.
DR GeneID; 4352398; -.
DR Gramene; Os12t0530000-01; Os12t0530000-01; Os12g0530000.
DR KEGG; osa:4352398; -.
DR eggNOG; KOG1756; Eukaryota.
DR HOGENOM; CLU_062828_3_0_1; -.
DR InParanoid; Q2QPG9; -.
DR OMA; VMPYIHP; -.
DR OrthoDB; 1504122at2759; -.
DR Proteomes; UP000000763; Chromosome 12.
DR Proteomes; UP000059680; Chromosome 12.
DR Genevisible; Q2QPG9; OS.
DR GO; GO:0000786; C:nucleosome; IEA:UniProtKB-KW.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
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 2: Evidence at transcript level;
KW Chromosome; DNA-binding; Nucleosome core; Nucleus; Phosphoprotein;
KW Reference proteome.
FT CHAIN 1..138
FT /note="Probable histone H2AXb"
FT /id="PRO_0000239999"
FT REGION 1..24
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 135..136
FT /note="[ST]-Q motif"
FT MOD_RES 135
FT /note="Phosphoserine; by ATM and ATR"
FT /evidence="ECO:0000305"
SQ SEQUENCE 138 AA; 14339 MW; D22F6DAF5B3679FF CRC64;
MSSAGGGGGR GKSKGSKSVS RSSKAGLQFP VGRIARYLKA GKYAERVGAG APVYLSAVLE
YLAAEVLELA GNAARDNKKN RIVPRHIQLA VRNDEELSRL LGAVTIAAGG VLPNIHQTLL
PKKGGKDKAD IGSASQEF
