HMGB4_ARATH
ID HMGB4_ARATH Reviewed; 138 AA.
AC Q42344; B9DG70; O49598; Q2V484; Q8LCY0; Q94K96;
DT 02-NOV-2010, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 153.
DE RecName: Full=High mobility group B protein 4;
DE AltName: Full=High mobility group protein G;
DE Short=AtHMGgamma;
DE Short=HMG gamma;
DE AltName: Full=Nucleosome/chromatin assembly factor group D 04;
DE Short=Nucleosome/chromatin assembly factor group D 4;
GN Name=HMGB4; Synonyms=HMGG, HMGGAMMA, NFD04, NFD4;
GN OrderedLocusNames=At2g17560; ORFNames=MJB20.12;
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 [MRNA] (ISOFORM 1), FUNCTION, AND TISSUE SPECIFICITY.
RC TISSUE=Leaf;
RX PubMed=9461286; DOI=10.1111/j.1432-1033.1997.00646.x;
RA Stemmer C., Ritt C., Igloi G.L., Grimm R., Grasser K.D.;
RT "Variability in Arabidopsis thaliana chromosomal high-mobility-group-1-like
RT proteins.";
RL Eur. J. Biochem. 250:646-652(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia; TISSUE=Protoplast;
RA Cooke R., Laudie M., Raynal M., Delseny M.;
RT "The Arabidopsis thaliana transcribed genome: the GDR cDNA program.";
RL Submitted (NOV-1993) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
RN [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
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 [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=cv. Columbia; TISSUE=Rosette leaf;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
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 [8]
RP PHOSPHORYLATION.
RX PubMed=12653554; DOI=10.1021/bi027350d;
RA Stemmer C., Leeming D.J., Franssen L., Grimm R., Grasser K.D.;
RT "Phosphorylation of maize and Arabidopsis HMGB proteins by protein kinase
RT CK2alpha.";
RL Biochemistry 42:3503-3508(2003).
RN [9]
RP TISSUE SPECIFICITY, AND INDUCTION BY COLD.
RX PubMed=17169924; DOI=10.1093/pcp/pcl057;
RA Kwak K.J., Kim J.Y., Kim Y.O., Kang H.;
RT "Characterization of transgenic Arabidopsis plants overexpressing high
RT mobility group B proteins under high salinity, drought or cold stress.";
RL Plant Cell Physiol. 48:221-231(2007).
RN [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-130, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Columbia;
RX PubMed=19245862; DOI=10.1016/j.jprot.2009.02.004;
RA Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A., Andreasson E.,
RA Rathjen J.P., Peck S.C.;
RT "Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis
RT thaliana.";
RL J. Proteomics 72:439-451(2009).
RN [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-130, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [12]
RP REVIEW, AND SUBCELLULAR LOCATION.
RX PubMed=20123078; DOI=10.1016/j.bbagrm.2009.11.004;
RA Pedersen D.S., Grasser K.D.;
RT "The role of chromosomal HMGB proteins in plants.";
RL Biochim. Biophys. Acta 1799:171-174(2010).
CC -!- FUNCTION: Binds preferentially double-stranded DNA.
CC {ECO:0000269|PubMed:9461286}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00267,
CC ECO:0000269|PubMed:20123078}. Cytoplasm, cytosol
CC {ECO:0000269|PubMed:20123078}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q42344-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q42344-2; Sequence=VSP_039944;
CC -!- TISSUE SPECIFICITY: Mostly expressed roots and flowers, and, to a lower
CC extent, in stems and leaves. {ECO:0000269|PubMed:17169924,
CC ECO:0000269|PubMed:9461286}.
CC -!- INDUCTION: Up-regulated by cold stress. {ECO:0000269|PubMed:17169924}.
CC -!- SIMILARITY: Belongs to the HMGB family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; Y14074; CAA74403.1; -; mRNA.
DR EMBL; F20020; CAA23382.1; -; mRNA.
DR EMBL; AC007584; AAD32913.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC06651.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC06652.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC06653.1; -; Genomic_DNA.
DR EMBL; AF370150; AAK43965.1; -; mRNA.
DR EMBL; AF370562; AAK49570.1; -; mRNA.
DR EMBL; AY150467; AAN12992.1; -; mRNA.
DR EMBL; AK317044; BAH19737.1; -; mRNA.
DR EMBL; AY086336; AAM64404.1; -; mRNA.
DR PIR; F84553; F84553.
DR PIR; T51596; T51596.
DR RefSeq; NP_001031364.2; NM_001036287.3. [Q42344-1]
DR RefSeq; NP_001077909.1; NM_001084440.1. [Q42344-2]
DR RefSeq; NP_179347.1; NM_127310.3. [Q42344-1]
DR AlphaFoldDB; Q42344; -.
DR SMR; Q42344; -.
DR BioGRID; 1620; 6.
DR IntAct; Q42344; 4.
DR STRING; 3702.AT2G17560.1; -.
DR iPTMnet; Q42344; -.
DR PaxDb; Q42344; -.
DR PRIDE; Q42344; -.
DR ProteomicsDB; 232097; -. [Q42344-1]
DR EnsemblPlants; AT2G17560.1; AT2G17560.1; AT2G17560. [Q42344-1]
DR EnsemblPlants; AT2G17560.2; AT2G17560.2; AT2G17560. [Q42344-1]
DR EnsemblPlants; AT2G17560.3; AT2G17560.3; AT2G17560. [Q42344-2]
DR GeneID; 816263; -.
DR Gramene; AT2G17560.1; AT2G17560.1; AT2G17560. [Q42344-1]
DR Gramene; AT2G17560.2; AT2G17560.2; AT2G17560. [Q42344-1]
DR Gramene; AT2G17560.3; AT2G17560.3; AT2G17560. [Q42344-2]
DR KEGG; ath:AT2G17560; -.
DR Araport; AT2G17560; -.
DR TAIR; locus:2053893; AT2G17560.
DR eggNOG; KOG0381; Eukaryota.
DR InParanoid; Q42344; -.
DR OMA; NTFKRPP; -.
DR OrthoDB; 1641977at2759; -.
DR PhylomeDB; Q42344; -.
DR PRO; PR:Q42344; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q42344; baseline and differential.
DR Genevisible; Q42344; AT.
DR GO; GO:0000785; C:chromatin; TAS:TAIR.
DR GO; GO:0005737; C:cytoplasm; IDA:TAIR.
DR GO; GO:0005829; C:cytosol; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0003682; F:chromatin binding; TAS:TAIR.
DR GO; GO:0003677; F:DNA binding; IDA:TAIR.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; ISS:TAIR.
DR GO; GO:0030527; F:structural constituent of chromatin; TAS:TAIR.
DR GO; GO:0006325; P:chromatin organization; TAS:TAIR.
DR Gene3D; 1.10.30.10; -; 1.
DR InterPro; IPR009071; HMG_box_dom.
DR InterPro; IPR036910; HMG_box_dom_sf.
DR InterPro; IPR031061; HMGB_plant.
DR PANTHER; PTHR46261; PTHR46261; 1.
DR Pfam; PF00505; HMG_box; 1.
DR SMART; SM00398; HMG; 1.
DR SUPFAM; SSF47095; SSF47095; 1.
DR PROSITE; PS50118; HMG_BOX_2; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Cytoplasm; DNA-binding; Nucleus; Phosphoprotein;
KW Reference proteome.
FT CHAIN 1..138
FT /note="High mobility group B protein 4"
FT /id="PRO_0000399930"
FT DNA_BIND 35..104
FT /note="HMG box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00267"
FT REGION 1..41
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 105..138
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..19
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 110..127
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 123
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O49595"
FT MOD_RES 130
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19245862,
FT ECO:0007744|PubMed:19376835"
FT VAR_SEQ 129..132
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:19423640"
FT /id="VSP_039944"
FT CONFLICT 9
FT /note="E -> G (in Ref. 1; CAA74403)"
FT /evidence="ECO:0000305"
FT CONFLICT 26
FT /note="K -> N (in Ref. 7; AAM64404)"
FT /evidence="ECO:0000305"
FT CONFLICT 76
FT /note="A -> S (in Ref. 7; AAM64404 and 1; CAA74403)"
FT /evidence="ECO:0000305"
FT CONFLICT 92
FT /note="R -> I (in Ref. 5; AAK43965)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 138 AA; 15420 MW; DCACFC5DED52D3C7 CRC64;
MKGGESKAEA TSTDQRLKTR GRKAGKKTKK DPNQPKRPPS AFFVFLEDFR KEFNLANPNN
KSVATVGKAA GARWKAMTDE DKAPYVAKAE SRKTEYIKNV QQYNLKLASG TNREEDDSDK
SKSEVDEAVS EEEAEDDD
