H2A6_ARATH
ID H2A6_ARATH Reviewed; 130 AA.
AC Q9LD28;
DT 30-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 137.
DE RecName: Full=Histone H2A.6;
DE AltName: Full=HTA1;
DE AltName: Full=Protein RESISTANT TO AGROBACTERIUM TRANSFORMATION 5;
GN Name=RAT5; Synonyms=H2A-1; OrderedLocusNames=At5g54640; ORFNames=MRB17.14;
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 [GENOMIC DNA], AND FUNCTION.
RC STRAIN=cv. Wassilewskija;
RX PubMed=10639185; DOI=10.1073/pnas.97.2.948;
RA Mysore K.S., Nam J., Gelvin S.B.;
RT "An Arabidopsis histone H2A mutant is deficient in Agrobacterium T-DNA
RT integration.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:948-953(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9872454; DOI=10.1093/dnares/5.5.297;
RA Nakamura Y., Sato S., Asamizu E., Kaneko T., Kotani H., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. VII. Sequence
RT features of the regions of 1,013,767 bp covered by sixteen physically
RT assigned P1 and TAC clones.";
RL DNA Res. 5:297-308(1998).
RN [3]
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 [4]
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 [5]
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 [6]
RP FUNCTION, TISSUE SPECIFICITY, AND INDUCTION.
RX PubMed=12410808; DOI=10.1046/j.1365-313x.2002.01425.x;
RA Yi H., Mysore K.S., Gelvin S.B.;
RT "Expression of the Arabidopsis histone H2A-1 gene correlates with
RT susceptibility to Agrobacterium transformation.";
RL Plant J. 32:285-298(2002).
RN [7]
RP INTERACTION WITH VIP1.
RC STRAIN=cv. Columbia;
RX PubMed=15824315; DOI=10.1073/pnas.0404118102;
RA Li J., Krichevsky A., Vaidya M., Tzfira T., Citovsky V.;
RT "Uncoupling of the functions of the Arabidopsis VIP1 protein in transient
RT and stable plant genetic transformation by Agrobacterium.";
RL Proc. Natl. Acad. Sci. U.S.A. 102:5733-5738(2005).
RN [8]
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).
RN [9]
RP LACK OF UBIQUITINATION, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=17554311; DOI=10.1038/nature05864;
RA Sridhar V.V., Kapoor A., Zhang K., Zhu J., Zhou T., Hasegawa P.M.,
RA Bressan R.A., Zhu J.-K.;
RT "Control of DNA methylation and heterochromatic silencing by histone H2B
RT deubiquitination.";
RL Nature 447:735-738(2007).
CC -!- FUNCTION: Core component of nucleosome. Nucleosomes wrap and compact
CC DNA into chromatin, limiting DNA accessibility to the cellular
CC machineries which require DNA as a template. Histones thereby play a
CC central role in transcription regulation, DNA repair, DNA replication
CC and chromosomal stability. DNA accessibility is regulated via a complex
CC set of post-translational modifications of histones, also called
CC histone code, and nucleosome remodeling. Required for the T-DNA
CC integration step of plant transformation by Agrobacterium. May play an
CC important role in illegitimate recombination.
CC {ECO:0000269|PubMed:10639185, ECO:0000269|PubMed:12410808}.
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 VIP1. {ECO:0000269|PubMed:15824315}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}. Chromosome {ECO:0000250}.
CC -!- TISSUE SPECIFICITY: Low level of expression, mainly in dividing
CC tissues: floral buds, margins of newly emerging leaves, expanding
CC leaves and the meristematic zone of root tips. Also expressed in many
CC non-dividing cells of the elongation zone of the root.
CC {ECO:0000269|PubMed:12410808, ECO:0000269|PubMed:16751347}.
CC -!- INDUCTION: By phytohormones. Transiently by wounding.
CC {ECO:0000269|PubMed:12410808}.
CC -!- PTM: Not ubiquitinated.
CC -!- MISCELLANEOUS: RAT5 is required for Agrobacterium-mediated
CC transformation of root but not of germ-lime tissues.
CC -!- SIMILARITY: Belongs to the histone H2A family. {ECO:0000305}.
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DR EMBL; AF204968; AAF64419.1; -; Genomic_DNA.
DR EMBL; AB016879; BAB09343.1; -; Genomic_DNA.
DR EMBL; CP002688; AED96521.1; -; Genomic_DNA.
DR EMBL; AF204967; AAF64418.1; -; Genomic_DNA.
DR EMBL; BT004023; AAO42059.1; -; mRNA.
DR EMBL; BT005189; AAO50722.1; -; mRNA.
DR EMBL; AY088261; AAM65801.1; -; mRNA.
DR RefSeq; NP_200275.1; NM_124845.4.
DR PDB; 7BP2; X-ray; 1.58 A; A/C=14-106.
DR PDB; 7BP4; X-ray; 2.10 A; A/G=14-106.
DR PDB; 7BP5; X-ray; 1.90 A; A=14-106.
DR PDB; 7BP6; X-ray; 1.58 A; C=14-106.
DR PDB; 7C7X; X-ray; 3.00 A; A/C=14-106.
DR PDBsum; 7BP2; -.
DR PDBsum; 7BP4; -.
DR PDBsum; 7BP5; -.
DR PDBsum; 7BP6; -.
DR PDBsum; 7C7X; -.
DR AlphaFoldDB; Q9LD28; -.
DR SMR; Q9LD28; -.
DR BioGRID; 20797; 6.
DR IntAct; Q9LD28; 4.
DR STRING; 3702.AT5G54640.1; -.
DR PaxDb; Q9LD28; -.
DR PRIDE; Q9LD28; -.
DR ProteomicsDB; 230122; -.
DR EnsemblPlants; AT5G54640.1; AT5G54640.1; AT5G54640.
DR GeneID; 835553; -.
DR Gramene; AT5G54640.1; AT5G54640.1; AT5G54640.
DR KEGG; ath:AT5G54640; -.
DR Araport; AT5G54640; -.
DR TAIR; locus:2172119; AT5G54640.
DR eggNOG; KOG1756; Eukaryota.
DR HOGENOM; CLU_062828_3_0_1; -.
DR InParanoid; Q9LD28; -.
DR OMA; VIVECAC; -.
DR OrthoDB; 1504122at2759; -.
DR PhylomeDB; Q9LD28; -.
DR PRO; PR:Q9LD28; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9LD28; baseline and differential.
DR Genevisible; Q9LD28; AT.
DR GO; GO:0005730; C:nucleolus; HDA:TAIR.
DR GO; GO:0000786; C:nucleosome; IEA:UniProtKB-KW.
DR GO; GO:0009536; C:plastid; HDA: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 GO; GO:0009294; P:DNA-mediated transformation; IMP:TAIR.
DR GO; GO:0009617; P:response to bacterium; IEP:TAIR.
DR GO; GO:0009611; P:response to wounding; IEP:TAIR.
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 3D-structure; Chromosome; DNA-binding; Nucleosome core; Nucleus;
KW Reference proteome.
FT CHAIN 1..130
FT /note="Histone H2A.6"
FT /id="PRO_0000238450"
FT REGION 1..23
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT HELIX 19..23
FT /evidence="ECO:0007829|PDB:7BP2"
FT HELIX 29..38
FT /evidence="ECO:0007829|PDB:7BP2"
FT STRAND 42..45
FT /evidence="ECO:0007829|PDB:7BP2"
FT HELIX 48..74
FT /evidence="ECO:0007829|PDB:7BP2"
FT STRAND 78..80
FT /evidence="ECO:0007829|PDB:7BP2"
FT HELIX 82..90
FT /evidence="ECO:0007829|PDB:7BP2"
FT HELIX 93..99
FT /evidence="ECO:0007829|PDB:7BP2"
SQ SEQUENCE 130 AA; 13658 MW; 5EB8EB78821D4F81 CRC64;
MAGRGKTLGS GGAKKATSRS SKAGLQFPVG RIARFLKAGK YAERVGAGAP VYLAAVLEYL
AAEVLELAGN AARDNKKTRI VPRHIQLAVR NDEELSKLLG DVTIANGGVM PNIHNLLLPK
KAGASKPQED
