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Protein

Probable histone H2AXa

Gene

At1g08880

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Variant histone H2A which replaces conventional H2A in a subset of nucleosomes. 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. Required for checkpoint-mediated arrest of cell cycle progression in response to low doses of ionizing radiation and for efficient repair of DNA double strand breaks (DSBs) specifically when modified by C-terminal phosphorylation (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Probable histone H2AXa
Alternative name(s):
HTA5
Gene namesi
Ordered Locus Names:At1g08880
ORF Names:F7G19.24
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 1

Organism-specific databases

TAIRiAT1G08880.

Subcellular locationi

GO - Cellular componenti

  • nuclear chromatin Source: GO_Central
  • nucleosome Source: UniProtKB-KW
  • nucleus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 142142Probable histone H2AXaPRO_0000055197Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei139 – 1391Phosphoserine; by ATM and ATR1 Publication

Post-translational modificationi

Phosphorylated to form H2AXS139ph (gamma-H2AX) in response to DNA double strand breaks (DSBs) generated by exogenous genotoxic agents and by stalled replication forks, and may also occur during meiotic recombination events. Phosphorylation can extend up to several thousand nucleosomes from the actual site of the DSB and may mark the surrounding chromatin for recruitment of proteins required for DNA damage signaling and repair. Widespread phosphorylation may also serve to amplify the damage signal or aid repair of persistent lesions. H2AXS139ph in response to ionizing radiation is mediated by ATM while defects in DNA replication induce H2AXS139ph subsequent to activation of ATR. Dephosphorylation of H2AXS139ph by PP2A is required for DNA DSB repair (By similarity).By similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiO04848.
PRIDEiO04848.

PTM databases

iPTMnetiO04848.

Expressioni

Tissue specificityi

Expressed mainly in roots.1 Publication

Gene expression databases

GenevisibleiO04848. AT.

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 numerous proteins required for DNA damage signaling and repair when phosphorylated on Ser-139 (By similarity).By similarity

Protein-protein interaction databases

STRINGi3702.AT1G08880.1.

Structurei

3D structure databases

ProteinModelPortaliO04848.
SMRiO04848. Positions 26-125.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi139 – 1402[ST]-Q motif

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

eggNOGiKOG1756. Eukaryota.
COG5262. LUCA.
HOGENOMiHOG000234652.
InParanoidiO04848.
KOiK11251.
OMAiYAPRVES.
PhylomeDBiO04848.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR002119. Histone_H2A.
IPR007125. Histone_H2A/H2B/H3.
IPR032454. Histone_H2A_C.
IPR032458. Histone_H2A_CS.
[Graphical view]
PfamiPF00125. Histone. 1 hit.
PF16211. Histone_H2A_C. 1 hit.
[Graphical view]
PRINTSiPR00620. HISTONEH2A.
SMARTiSM00414. H2A. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00046. HISTONE_H2A. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O04848-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTGAGSGTT KGGRGKPKAT KSVSRSSKAG LQFPVGRIAR FLKSGKYAER
60 70 80 90 100
VGAGAPVYLS AVLEYLAAEV LELAGNAARD NKKTRIVPRH IQLAVRNDEE
110 120 130 140
LSKLLGSVTI ANGGVLPNIH QTLLPSKVGK NKGDIGSASQ EF
Length:142
Mass (Da):14,813
Last modified:July 1, 1997 - v1
Checksum:i84ECDF2E5E46A3F9
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti39 – 391A → AL in AAM65474 (Ref. 4) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC000106 Genomic DNA. Translation: AAB70416.1.
CP002684 Genomic DNA. Translation: AEE28361.1.
AY093975 mRNA. Translation: AAM16236.1.
AF412092 mRNA. Translation: AAL06545.1.
AY087924 mRNA. Translation: AAM65474.1.
PIRiE86220.
RefSeqiNP_172363.1. NM_100760.4.
UniGeneiAt.24300.

Genome annotation databases

EnsemblPlantsiAT1G08880.1; AT1G08880.1; AT1G08880.
GeneIDi837409.
GrameneiAT1G08880.1; AT1G08880.1; AT1G08880.
KEGGiath:AT1G08880.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC000106 Genomic DNA. Translation: AAB70416.1.
CP002684 Genomic DNA. Translation: AEE28361.1.
AY093975 mRNA. Translation: AAM16236.1.
AF412092 mRNA. Translation: AAL06545.1.
AY087924 mRNA. Translation: AAM65474.1.
PIRiE86220.
RefSeqiNP_172363.1. NM_100760.4.
UniGeneiAt.24300.

3D structure databases

ProteinModelPortaliO04848.
SMRiO04848. Positions 26-125.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT1G08880.1.

PTM databases

iPTMnetiO04848.

Proteomic databases

PaxDbiO04848.
PRIDEiO04848.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT1G08880.1; AT1G08880.1; AT1G08880.
GeneIDi837409.
GrameneiAT1G08880.1; AT1G08880.1; AT1G08880.
KEGGiath:AT1G08880.

Organism-specific databases

TAIRiAT1G08880.

Phylogenomic databases

eggNOGiKOG1756. Eukaryota.
COG5262. LUCA.
HOGENOMiHOG000234652.
InParanoidiO04848.
KOiK11251.
OMAiYAPRVES.
PhylomeDBiO04848.

Miscellaneous databases

PROiO04848.

Gene expression databases

GenevisibleiO04848. AT.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR002119. Histone_H2A.
IPR007125. Histone_H2A/H2B/H3.
IPR032454. Histone_H2A_C.
IPR032458. Histone_H2A_CS.
[Graphical view]
PfamiPF00125. Histone. 1 hit.
PF16211. Histone_H2A_C. 1 hit.
[Graphical view]
PRINTSiPR00620. HISTONEH2A.
SMARTiSM00414. H2A. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00046. HISTONE_H2A. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
    Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
    , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
    Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  2. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  3. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  4. "Full-length cDNA from Arabidopsis thaliana."
    Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
    Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  5. "Ionizing radiation-dependent gamma-H2AX focus formation requires ataxia telangiectasia mutated and ataxia telangiectasia mutated and Rad3-related."
    Friesner J.D., Liu B., Culligan K., Britt A.B.
    Mol. Biol. Cell 16:2566-2576(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION.
  6. "Constitutive expression exposes functional redundancy between the Arabidopsis histone H2A gene HTA1 and other H2A gene family members."
    Yi H., Sardesai N., Fujinuma T., Chan C.-W., Veena X., Gelvin S.B.
    Plant Cell 18:1575-1589(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, NOMENCLATURE.

Entry informationi

Entry nameiH2AXA_ARATH
AccessioniPrimary (citable) accession number: O04848
Secondary accession number(s): Q8LAC0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 7, 2006
Last sequence update: July 1, 1997
Last modified: February 17, 2016
This is version 114 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant 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: H2AXS139ph = phosphorylated Ser-139.Curated

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.