HMGB5_ARATH
ID HMGB5_ARATH Reviewed; 125 AA.
AC O49597;
DT 02-NOV-2010, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1998, sequence version 1.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=High mobility group B protein 5;
DE AltName: Full=High mobility group protein D;
DE Short=AtHMGdelta;
DE Short=HMG delta;
DE AltName: Full=Nucleosome/chromatin assembly factor group D 05;
DE Short=Nucleosome/chromatin assembly factor group D 5;
GN Name=HMGB5; Synonyms=HMGD, HMGDELTA, NFD05, NFD5;
GN OrderedLocusNames=At4g35570; ORFNames=F8D20.80;
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], 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 GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
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; 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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Quinitio C., Chen H., Kim C.J., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (MAY-2006) to the EMBL/GenBank/DDBJ databases.
RN [6]
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 [7]
RP SUBCELLULAR LOCATION.
RX PubMed=17114349; DOI=10.1105/tpc.106.047274;
RA Launholt D., Merkle T., Houben A., Schulz A., Grasser K.D.;
RT "Arabidopsis chromatin-associated HMGA and HMGB use different nuclear
RT targeting signals and display highly dynamic localization within the
RT nucleus.";
RL Plant Cell 18:2904-2918(2006).
RN [8]
RP TISSUE SPECIFICITY.
RX PubMed=17316617; DOI=10.1016/j.febslet.2007.02.015;
RA Launholt D., Groenlund J.T., Nielsen H.K., Grasser K.D.;
RT "Overlapping expression patterns among the genes encoding Arabidopsis
RT chromosomal high mobility group (HMG) proteins.";
RL FEBS Lett. 581:1114-1118(2007).
RN [9]
RP FUNCTION, AND TISSUE SPECIFICITY.
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 REVIEW.
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. Confers resistance
CC to salt and drought stresses. {ECO:0000269|PubMed:17169924,
CC ECO:0000269|PubMed:9461286}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00267,
CC ECO:0000269|PubMed:17114349}. Note=Displays a highly dynamic speckle
CC distribution pattern in interphase chromatin.
CC -!- TISSUE SPECIFICITY: Mostly expressed lateral roots, root tips and
CC flowers (including pedicels, but excluding ovary), and, to a lower
CC extent, in cotyledons, hypocotyls, stems and leaves.
CC {ECO:0000269|PubMed:17169924, ECO:0000269|PubMed:17316617,
CC ECO:0000269|PubMed:9461286}.
CC -!- SIMILARITY: Belongs to the HMGB family. {ECO:0000305}.
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DR EMBL; Y14075; CAA74404.1; -; mRNA.
DR EMBL; AL031135; CAA20027.1; -; Genomic_DNA.
DR EMBL; AL161587; CAB80273.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE86532.1; -; Genomic_DNA.
DR EMBL; CP002687; ANM68018.1; -; Genomic_DNA.
DR EMBL; AK317173; BAH19859.1; -; mRNA.
DR EMBL; BT025597; ABF59015.1; -; mRNA.
DR EMBL; AY085615; AAM62836.1; -; mRNA.
DR PIR; T04662; T04662.
DR RefSeq; NP_001329802.1; NM_001342361.1.
DR RefSeq; NP_195282.1; NM_119722.3.
DR AlphaFoldDB; O49597; -.
DR SMR; O49597; -.
DR BioGRID; 14991; 6.
DR IntAct; O49597; 5.
DR STRING; 3702.AT4G35570.1; -.
DR MetOSite; O49597; -.
DR PaxDb; O49597; -.
DR PRIDE; O49597; -.
DR ProteomicsDB; 228804; -.
DR EnsemblPlants; AT4G35570.1; AT4G35570.1; AT4G35570.
DR EnsemblPlants; AT4G35570.2; AT4G35570.2; AT4G35570.
DR GeneID; 829709; -.
DR Gramene; AT4G35570.1; AT4G35570.1; AT4G35570.
DR Gramene; AT4G35570.2; AT4G35570.2; AT4G35570.
DR KEGG; ath:AT4G35570; -.
DR Araport; AT4G35570; -.
DR TAIR; locus:2128003; AT4G35570.
DR eggNOG; KOG0381; Eukaryota.
DR HOGENOM; CLU_082854_1_1_1; -.
DR InParanoid; O49597; -.
DR OMA; QQYNMEL; -.
DR OrthoDB; 1641977at2759; -.
DR PhylomeDB; O49597; -.
DR PRO; PR:O49597; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; O49597; baseline and differential.
DR Genevisible; O49597; AT.
DR GO; GO:0000785; C:chromatin; TAS:TAIR.
DR GO; GO:0005737; C:cytoplasm; IDA:TAIR.
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 2: Evidence at transcript level;
KW DNA-binding; Nucleus; Reference proteome.
FT CHAIN 1..125
FT /note="High mobility group B protein 5"
FT /id="PRO_0000399931"
FT DNA_BIND 34..103
FT /note="HMG box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00267"
FT REGION 1..40
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 106..125
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..34
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 111..125
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 125 AA; 14203 MW; 9C6C268C4D3A0FDF CRC64;
MKDNQTEVES RSTDDRLKVR GNKVGKKTKD PNRPKKPPSP FFVFLDDFRK EFNLANPDNK
SVGNVGRAAG KKWKTMTEEE RAPFVAKSQS KKTEYAVTMQ QYNMELANGN KTTGDDEKQE
KAADD
