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High mobility group B protein 1 (High mobility group protein A) (AtHMGalpha) (HMG alpha) (Nucleosome/chromatin assembly factor group D 01) (Nucleosome/chromatin assembly factor group D 1)

 HMGB1_ARATH             Reviewed;         178 AA.
O49595; Q3EAL6;
02-NOV-2010, integrated into UniProtKB/Swiss-Prot.
01-JUN-1998, sequence version 1.
23-MAY-2018, entry version 124.
RecName: Full=High mobility group B protein 1;
AltName: Full=High mobility group protein A;
Short=AtHMGalpha;
Short=HMG alpha;
AltName: Full=Nucleosome/chromatin assembly factor group D 01;
Short=Nucleosome/chromatin assembly factor group D 1;
Name=HMGB1; Synonyms=HMGA, HMGALPHA, NFD01, NFD1, ORF13;
OrderedLocusNames=At3g51880; ORFNames=ATEM1.13;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, AND TISSUE
SPECIFICITY.
TISSUE=Leaf;
PubMed=9461286; DOI=10.1111/j.1432-1033.1997.00646.x;
Stemmer C., Ritt C., Igloi G.L., Grimm R., Grasser K.D.;
"Variability in Arabidopsis thaliana chromosomal high-mobility-group-
1-like proteins.";
Eur. J. Biochem. 250:646-652(1997).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10645728; DOI=10.1023/A:1006395324818;
Comella P., Wu H.-J., Laudie M., Berger C., Cooke R., Delseny M.,
Grellet F.;
"Fine sequence analysis of 60 kb around the Arabidopsis thaliana AtEm1
locus on chromosome III.";
Plant Mol. Biol. 41:687-700(1999).
[3]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
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.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
STRAIN=cv. Columbia; TISSUE=Rosette leaf;
PubMed=19423640; DOI=10.1093/dnares/dsp009;
Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M.,
Seki M., Shinozaki K.;
"Analysis of multiple occurrences of alternative splicing events in
Arabidopsis thaliana using novel sequenced full-length cDNAs.";
DNA Res. 16:155-164(2009).
[6]
PHOSPHORYLATION.
PubMed=12653554; DOI=10.1021/bi027350d;
Stemmer C., Leeming D.J., Franssen L., Grimm R., Grasser K.D.;
"Phosphorylation of maize and Arabidopsis HMGB proteins by protein
kinase CK2alpha.";
Biochemistry 42:3503-3508(2003).
[7]
SUBCELLULAR LOCATION, AND FUNCTION.
PubMed=17114349; DOI=10.1105/tpc.106.047274;
Launholt D., Merkle T., Houben A., Schulz A., Grasser K.D.;
"Arabidopsis chromatin-associated HMGA and HMGB use different nuclear
targeting signals and display highly dynamic localization within the
nucleus.";
Plant Cell 18:2904-2918(2006).
[8]
TISSUE SPECIFICITY.
PubMed=17316617; DOI=10.1016/j.febslet.2007.02.015;
Launholt D., Groenlund J.T., Nielsen H.K., Grasser K.D.;
"Overlapping expression patterns among the genes encoding Arabidopsis
chromosomal high mobility group (HMG) proteins.";
FEBS Lett. 581:1114-1118(2007).
[9]
TISSUE SPECIFICITY, AND INDUCTION BY SALT.
PubMed=17169924; DOI=10.1093/pcp/pcl057;
Kwak K.J., Kim J.Y., Kim Y.O., Kang H.;
"Characterization of transgenic Arabidopsis plants overexpressing high
mobility group B proteins under high salinity, drought or cold
stress.";
Plant Cell Physiol. 48:221-231(2007).
[10]
SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
PubMed=18822296; DOI=10.1016/j.jmb.2008.09.014;
Lildballe D.L., Pedersen D.S., Kalamajka R., Emmersen J., Houben A.,
Grasser K.D.;
"The expression level of the chromatin-associated HMGB1 protein
influences growth, stress tolerance, and transcriptome in
Arabidopsis.";
J. Mol. Biol. 384:9-21(2008).
[11]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-146, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Root;
PubMed=18433157; DOI=10.1021/pr8000173;
de la Fuente van Bentem S., Anrather D., Dohnal I., Roitinger E.,
Csaszar E., Joore J., Buijnink J., Carreri A., Forzani C.,
Lorkovic Z.J., Barta A., Lecourieux D., Verhounig A., Jonak C.,
Hirt H.;
"Site-specific phosphorylation profiling of Arabidopsis proteins by
mass spectrometry and peptide chip analysis.";
J. Proteome Res. 7:2458-2470(2008).
[12]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-146, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=cv. Columbia;
PubMed=19245862; DOI=10.1016/j.jprot.2009.02.004;
Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A.,
Andreasson E., Rathjen J.P., Peck S.C.;
"Phosphoproteomic analysis of nuclei-enriched fractions from
Arabidopsis thaliana.";
J. Proteomics 72:439-451(2009).
[13]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-137 AND SER-146, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19376835; DOI=10.1104/pp.109.138677;
Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
Grossmann J., Gruissem W., Baginsky S.;
"Large-scale Arabidopsis phosphoproteome profiling reveals novel
chloroplast kinase substrates and phosphorylation networks.";
Plant Physiol. 150:889-903(2009).
[14]
REVIEW.
PubMed=20123078; DOI=10.1016/j.bbagrm.2009.11.004;
Pedersen D.S., Grasser K.D.;
"The role of chromosomal HMGB proteins in plants.";
Biochim. Biophys. Acta 1799:171-174(2010).
-!- FUNCTION: Binds preferentially double-stranded DNA. Modulates
general plant growth and stress tolerance. Confers sensitivity to
salt and genotoxic (methyl methanesulfonate, MMS) stresses.
{ECO:0000269|PubMed:17114349, ECO:0000269|PubMed:9461286}.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-
ProRule:PRU00267, ECO:0000269|PubMed:17114349,
ECO:0000269|PubMed:18822296}. Note=Displays a highly dynamic
speckle distribution pattern in interphase chromatin but does not
associate with mitotic chromosomes.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=O49595-1; Sequence=Displayed;
Name=2;
IsoId=O49595-2; Sequence=VSP_039939;
Note=No experimental confirmation available.;
-!- TISSUE SPECIFICITY: Expressed in cotyledons, roots, stems, leaves
and flowers (excluding pedicels). {ECO:0000269|PubMed:17169924,
ECO:0000269|PubMed:17316617, ECO:0000269|PubMed:9461286}.
-!- INDUCTION: Down-regulated by salt stress.
{ECO:0000269|PubMed:17169924}.
-!- DISRUPTION PHENOTYPE: Slightly delayed and reduced germination
rate. Reduced root length. Enhanced sensitivity to methyl
methanesulfonate (MMS). {ECO:0000269|PubMed:18822296}.
-!- SIMILARITY: Belongs to the HMGB family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; Y14071; CAA74400.1; -; mRNA.
EMBL; AF049236; AAC14415.1; -; Genomic_DNA.
EMBL; CP002686; AEE78855.1; -; Genomic_DNA.
EMBL; CP002686; AEE78856.1; -; Genomic_DNA.
EMBL; CP002686; AEE78857.1; -; Genomic_DNA.
EMBL; CP002686; ANM65542.1; -; Genomic_DNA.
EMBL; AY056373; AAL08229.1; -; mRNA.
EMBL; AY113172; AAM47475.1; -; mRNA.
EMBL; AK316819; BAH19531.1; -; mRNA.
PIR; T51159; T51159.
RefSeq; NP_001078269.1; NM_001084800.2. [O49595-1]
RefSeq; NP_001327501.1; NM_001339538.1. [O49595-1]
RefSeq; NP_190756.1; NM_115047.3. [O49595-1]
RefSeq; NP_974413.1; NM_202684.3. [O49595-2]
UniGene; At.27677; -.
UniGene; At.480; -.
ProteinModelPortal; O49595; -.
SMR; O49595; -.
IntAct; O49595; 4.
STRING; 3702.AT3G51880.2; -.
iPTMnet; O49595; -.
PaxDb; O49595; -.
PRIDE; O49595; -.
EnsemblPlants; AT3G51880.1; AT3G51880.1; AT3G51880. [O49595-1]
EnsemblPlants; AT3G51880.2; AT3G51880.2; AT3G51880. [O49595-2]
EnsemblPlants; AT3G51880.3; AT3G51880.3; AT3G51880. [O49595-1]
EnsemblPlants; AT3G51880.5; AT3G51880.5; AT3G51880. [O49595-1]
GeneID; 824351; -.
Gramene; AT3G51880.1; AT3G51880.1; AT3G51880. [O49595-1]
Gramene; AT3G51880.2; AT3G51880.2; AT3G51880. [O49595-2]
Gramene; AT3G51880.3; AT3G51880.3; AT3G51880. [O49595-1]
Gramene; AT3G51880.5; AT3G51880.5; AT3G51880. [O49595-1]
KEGG; ath:AT3G51880; -.
Araport; AT3G51880; -.
TAIR; locus:2074368; AT3G51880.
eggNOG; KOG0381; Eukaryota.
eggNOG; COG5648; LUCA.
HOGENOM; HOG000197860; -.
InParanoid; O49595; -.
KO; K10802; -.
OMA; EDFRTTF; -.
PhylomeDB; O49595; -.
PRO; PR:O49595; -.
Proteomes; UP000006548; Chromosome 3.
ExpressionAtlas; O49595; baseline and differential.
Genevisible; O49595; AT.
GO; GO:0000785; C:chromatin; TAS:TAIR.
GO; GO:0005634; C:nucleus; IDA:UniProtKB.
GO; GO:0003682; F:chromatin binding; TAS:TAIR.
GO; GO:0003677; F:DNA binding; IDA:TAIR.
GO; GO:0003700; F:DNA binding transcription factor activity; ISS:TAIR.
GO; GO:0030527; F:structural constituent of chromatin; TAS:TAIR.
GO; GO:0006333; P:chromatin assembly or disassembly; TAS:TAIR.
Gene3D; 1.10.30.10; -; 1.
InterPro; IPR009071; HMG_box_dom.
InterPro; IPR036910; HMG_box_dom_sf.
Pfam; PF00505; HMG_box; 1.
SMART; SM00398; HMG; 1.
SUPFAM; SSF47095; SSF47095; 1.
PROSITE; PS50118; HMG_BOX_2; 1.
1: Evidence at protein level;
Alternative splicing; Complete proteome; DNA-binding; Nucleus;
Phosphoprotein; Reference proteome.
CHAIN 1 178 High mobility group B protein 1.
/FTId=PRO_0000399927.
DNA_BIND 53 122 HMG box. {ECO:0000255|PROSITE-
ProRule:PRU00267}.
COMPBIAS 99 177 Glu-rich.
MOD_RES 137 137 Phosphoserine.
{ECO:0000244|PubMed:19376835}.
MOD_RES 146 146 Phosphoserine.
{ECO:0000244|PubMed:18433157,
ECO:0000244|PubMed:19245862,
ECO:0000244|PubMed:19376835}.
VAR_SEQ 148 148 E -> EVTIPLSN (in isoform 2).
{ECO:0000303|PubMed:19423640}.
/FTId=VSP_039939.
SEQUENCE 178 AA; 20265 MW; 2C1130786210828B CRC64;
MKTAKGKDKV KTTKEALKPV DDRKVGKRKA PAEKPTKRET RKEKKAKKDP NKPKRAPSAF
FVFLEDFRVT FKKENPNVKA VSAVGKAGGQ KWKSMSQAEK APYEEKAAKR KAEYEKQMDA
YNKNLEEGSD ESEKSRSEIN DEDEASGEEE LLEKEAAGDD EEEEEEEDDD DDDDEEED


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