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High mobility group protein B1 (High mobility group protein 1) (HMG-1)

 HMGB1_CHICK             Reviewed;         215 AA.
Q9YH06; H9BNX0; Q9PUK9;
18-SEP-2013, integrated into UniProtKB/Swiss-Prot.
01-MAY-1999, sequence version 1.
25-OCT-2017, entry version 119.
RecName: Full=High mobility group protein B1;
AltName: Full=High mobility group protein 1;
Short=HMG-1;
Name=HMGB1; Synonyms=HMG1; ORFNames=RCJMB04_15a21;
Gallus gallus (Chicken).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes;
Phasianidae; Phasianinae; Gallus.
NCBI_TaxID=9031;
[1]
NUCLEOTIDE SEQUENCE [MRNA].
TISSUE=B-cell;
PubMed=9931456; DOI=10.1016/S0378-1119(98)00542-3;
Lee K.B., Brooks D.J., Thomas J.O.;
"Selection of a cDNA clone for chicken high-mobility-group 1 (HMG1)
protein through its unusually conserved 3'-untranslated region, and
improved expression of recombinant HMG1 in Escherichia coli.";
Gene 225:97-105(1998).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=CB; TISSUE=Bursa of Fabricius;
PubMed=15642098; DOI=10.1186/gb-2004-6-1-r6;
Caldwell R.B., Kierzek A.M., Arakawa H., Bezzubov Y., Zaim J.,
Fiedler P., Kutter S., Blagodatski A., Kostovska D., Koter M.,
Plachy J., Carninci P., Hayashizaki Y., Buerstedde J.-M.;
"Full-length cDNAs from chicken bursal lymphocytes to facilitate gene
function analysis.";
Genome Biol. 6:R6.1-R6.9(2005).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=10978508; DOI=10.1016/S0167-4781(00)00164-0;
Lum H.K., Lee K.D., Yu G.;
"The chicken genome contains no HMG1 retropseudogenes but a functional
HMG1 gene with long introns.";
Biochim. Biophys. Acta 1493:64-72(2000).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=Red jungle fowl;
PubMed=15592404; DOI=10.1038/nature03154;
Hillier L.W., Miller W., Birney E., Warren W., Hardison R.C.,
Ponting C.P., Bork P., Burt D.W., Groenen M.A.M., Delany M.E.,
Dodgson J.B., Chinwalla A.T., Cliften P.F., Clifton S.W.,
Delehaunty K.D., Fronick C., Fulton R.S., Graves T.A., Kremitzki C.,
Layman D., Magrini V., McPherson J.D., Miner T.L., Minx P., Nash W.E.,
Nhan M.N., Nelson J.O., Oddy L.G., Pohl C.S., Randall-Maher J.,
Smith S.M., Wallis J.W., Yang S.-P., Romanov M.N., Rondelli C.M.,
Paton B., Smith J., Morrice D., Daniels L., Tempest H.G.,
Robertson L., Masabanda J.S., Griffin D.K., Vignal A., Fillon V.,
Jacobbson L., Kerje S., Andersson L., Crooijmans R.P., Aerts J.,
van der Poel J.J., Ellegren H., Caldwell R.B., Hubbard S.J.,
Grafham D.V., Kierzek A.M., McLaren S.R., Overton I.M., Arakawa H.,
Beattie K.J., Bezzubov Y., Boardman P.E., Bonfield J.K.,
Croning M.D.R., Davies R.M., Francis M.D., Humphray S.J., Scott C.E.,
Taylor R.G., Tickle C., Brown W.R.A., Rogers J., Buerstedde J.-M.,
Wilson S.A., Stubbs L., Ovcharenko I., Gordon L., Lucas S.,
Miller M.M., Inoko H., Shiina T., Kaufman J., Salomonsen J.,
Skjoedt K., Wong G.K.-S., Wang J., Liu B., Wang J., Yu J., Yang H.,
Nefedov M., Koriabine M., Dejong P.J., Goodstadt L., Webber C.,
Dickens N.J., Letunic I., Suyama M., Torrents D., von Mering C.,
Zdobnov E.M., Makova K., Nekrutenko A., Elnitski L., Eswara P.,
King D.C., Yang S.-P., Tyekucheva S., Radakrishnan A., Harris R.S.,
Chiaromonte F., Taylor J., He J., Rijnkels M., Griffiths-Jones S.,
Ureta-Vidal A., Hoffman M.M., Severin J., Searle S.M.J., Law A.S.,
Speed D., Waddington D., Cheng Z., Tuzun E., Eichler E., Bao Z.,
Flicek P., Shteynberg D.D., Brent M.R., Bye J.M., Huckle E.J.,
Chatterji S., Dewey C., Pachter L., Kouranov A., Mourelatos Z.,
Hatzigeorgiou A.G., Paterson A.H., Ivarie R., Brandstrom M.,
Axelsson E., Backstrom N., Berlin S., Webster M.T., Pourquie O.,
Reymond A., Ucla C., Antonarakis S.E., Long M., Emerson J.J.,
Betran E., Dupanloup I., Kaessmann H., Hinrichs A.S., Bejerano G.,
Furey T.S., Harte R.A., Raney B., Siepel A., Kent W.J., Haussler D.,
Eyras E., Castelo R., Abril J.F., Castellano S., Camara F., Parra G.,
Guigo R., Bourque G., Tesler G., Pevzner P.A., Smit A., Fulton L.A.,
Mardis E.R., Wilson R.K.;
"Sequence and comparative analysis of the chicken genome provide
unique perspectives on vertebrate evolution.";
Nature 432:695-716(2004).
[5]
NUCLEOTIDE SEQUENCE [MRNA] OF 1-185.
Sawant P.M., Dhama K., Wani M.Y., Upamanyu V., Singh S.D.,
Somvanshi R., Kumar P., Bisla S.R., Chaudhary D., Bassareddi M.;
Submitted (NOV-2011) to the EMBL/GenBank/DDBJ databases.
[6]
DOMAIN, AND SUBCELLULAR LOCATION.
PubMed=19102706; DOI=10.1021/bi8013449;
Kawase T., Sato K., Ueda T., Yoshida M.;
"Distinct domains in HMGB1 are involved in specific intramolecular and
nucleosomal interactions.";
Biochemistry 47:13991-13996(2008).
[7]
MUTAGENESIS OF LYS-3 AND LYS-12.
PubMed=18241198; DOI=10.1042/BJ20071613;
Assenberg R., Webb M., Connolly E., Stott K., Watson M., Hobbs J.,
Thomas J.O.;
"A critical role in structure-specific DNA binding for the
acetylatable lysine residues in HMGB1.";
Biochem. J. 411:553-561(2008).
-!- FUNCTION: Multifunctional redox sensitive protein with various
roles in different cellular compartments. Nuclear functions are
attributed to fully reduced HGMB1. Associates with chromatin and
binds DNA with a preference to non-canonical DNA structures such
as single-stranded DNA, DNA-containing cruciforms or bent
structures, supercoiled DNA and ZDNA. Can bent DNA and enhance DNA
flexibility by looping thus providing a mechanism to promote
activities on various gene promoters. Can restructure the
canonical nucleosome. Proposed to be an universal biosensor for
nucleic acids. May promote inflammatory response to sterile and
infectious signals and may be involved in the coordination and
integration of innate and adaptive immune responses. In the
cytoplasm may function as sensor and/or chaperone for immunogenic
nucleic acids, and mediate autophagy. May act as danger associated
molecular pattern (DAMP) molecule that amplifies immune responses
during tissue injury. {ECO:0000250|UniProtKB:P09429,
ECO:0000250|UniProtKB:P63158, ECO:0000250|UniProtKB:P63159}.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-
ProRule:PRU00267, ECO:0000305|PubMed:19102706}. Chromosome
{ECO:0000305|PubMed:19102706}. Cytoplasm {ECO:0000305}. Secreted
{ECO:0000305}.
-!- DOMAIN: The acidic C-terminal domain forms a flexible structure
which can reversibly interact intramolecularily with the HMG boxes
and modulate binding to DNA and other proteins; may involve Lys-3
and histone H3 'Lys-37' and 'Lys-38'.
{ECO:0000250|UniProtKB:P09429, ECO:0000250|UniProtKB:P63159,
ECO:0000269|PubMed:19102706}.
-!- PTM: Reduction/oxidation of cysteine residues Cys-23, Cys-45 and
Cys-106 and a possible intramolecular disulfide bond involving
Cys-23 and Cys-45 give rise to different redox forms with specific
functional activities: 1- fully reduced HMGB1
(HMGB1C23hC45hC106h), 2- disulfide HMGB1 (HMGB1C23-C45C106h) and
3- sulfonyl HMGB1 (HMGB1C23soC45soC106so).
{ECO:0000250|UniProtKB:P09429}.
-!- SIMILARITY: Belongs to the HMGB family. {ECO:0000305}.
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EMBL; Y17968; CAA76978.1; -; mRNA.
EMBL; AJ851648; CAH65282.1; -; mRNA.
EMBL; AF178849; AAD52670.1; -; Genomic_DNA.
EMBL; AADN03000868; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; AADN03001640; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; JQ040530; AFD33645.1; -; mRNA.
RefSeq; NP_990233.1; NM_204902.2.
RefSeq; XP_015133153.1; XM_015277667.1.
RefSeq; XP_015133156.1; XM_015277670.1.
UniGene; Gga.4638; -.
ProteinModelPortal; Q9YH06; -.
SMR; Q9YH06; -.
STRING; 9031.ENSGALP00000027541; -.
PaxDb; Q9YH06; -.
PRIDE; Q9YH06; -.
Ensembl; ENSGALT00000062837; ENSGALP00000047606; ENSGALG00000042875.
Ensembl; ENSGALT00000075072; ENSGALP00000044781; ENSGALG00000042875.
GeneID; 395724; -.
KEGG; gga:395724; -.
CTD; 3146; -.
eggNOG; KOG0381; Eukaryota.
eggNOG; COG5648; LUCA.
GeneTree; ENSGT00760000119164; -.
HOGENOM; HOG000197861; -.
HOVERGEN; HBG009000; -.
InParanoid; Q9YH06; -.
KO; K10802; -.
OMA; YSQDKRP; -.
OrthoDB; EOG091G0P81; -.
PhylomeDB; Q9YH06; -.
TreeFam; TF105371; -.
Reactome; R-GGA-211227; Activation of DNA fragmentation factor.
Reactome; R-GGA-5686938; Regulation of TLR by endogenous ligand.
Reactome; R-GGA-6798695; Neutrophil degranulation.
PRO; PR:Q9YH06; -.
Proteomes; UP000000539; Chromosome 1.
Bgee; ENSGALG00000017082; -.
GO; GO:0005623; C:cell; ISS:AgBase.
GO; GO:0009986; C:cell surface; IEA:Ensembl.
GO; GO:0000793; C:condensed chromosome; IEA:Ensembl.
GO; GO:0005769; C:early endosome; IEA:Ensembl.
GO; GO:0005615; C:extracellular space; IEA:Ensembl.
GO; GO:0043005; C:neuron projection; IEA:Ensembl.
GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
GO; GO:0017053; C:transcriptional repressor complex; IEA:Ensembl.
GO; GO:0000405; F:bubble DNA binding; IDA:AgBase.
GO; GO:0019958; F:C-X-C chemokine binding; IEA:Ensembl.
GO; GO:0010858; F:calcium-dependent protein kinase regulator activity; IEA:Ensembl.
GO; GO:0005125; F:cytokine activity; IEA:Ensembl.
GO; GO:0003684; F:damaged DNA binding; IEA:Ensembl.
GO; GO:0008301; F:DNA binding, bending; IDA:AgBase.
GO; GO:0070182; F:DNA polymerase binding; IEA:Ensembl.
GO; GO:0003725; F:double-stranded RNA binding; IEA:Ensembl.
GO; GO:0000400; F:four-way junction DNA binding; IDA:AgBase.
GO; GO:0001530; F:lipopolysaccharide binding; IEA:Ensembl.
GO; GO:0016829; F:lyase activity; IEA:Ensembl.
GO; GO:0044378; F:non-sequence-specific DNA binding, bending; ISS:AgBase.
GO; GO:0001786; F:phosphatidylserine binding; IEA:Ensembl.
GO; GO:0030295; F:protein kinase activator activity; IEA:Ensembl.
GO; GO:0070491; F:repressing transcription factor binding; IEA:Ensembl.
GO; GO:0003727; F:single-stranded RNA binding; IEA:Ensembl.
GO; GO:0097100; F:supercoiled DNA binding; IDA:AgBase.
GO; GO:0003700; F:transcription factor activity, sequence-specific DNA binding; IEA:Ensembl.
GO; GO:0002218; P:activation of innate immune response; IEA:Ensembl.
GO; GO:0043277; P:apoptotic cell clearance; IEA:Ensembl.
GO; GO:0006284; P:base-excision repair; IEA:Ensembl.
GO; GO:0031497; P:chromatin assembly; IEA:Ensembl.
GO; GO:0032392; P:DNA geometric change; IDA:AgBase.
GO; GO:0051103; P:DNA ligation involved in DNA repair; ISS:AgBase.
GO; GO:0035767; P:endothelial cell chemotaxis; IEA:Ensembl.
GO; GO:0001935; P:endothelial cell proliferation; IEA:Ensembl.
GO; GO:0001654; P:eye development; IEA:Ensembl.
GO; GO:0002437; P:inflammatory response to antigenic stimulus; IEA:Ensembl.
GO; GO:0045087; P:innate immune response; IEA:UniProtKB-KW.
GO; GO:0030324; P:lung development; IEA:Ensembl.
GO; GO:0002281; P:macrophage activation involved in immune response; IEA:Ensembl.
GO; GO:0001773; P:myeloid dendritic cell activation; IEA:Ensembl.
GO; GO:2000426; P:negative regulation of apoptotic cell clearance; IEA:Ensembl.
GO; GO:0043537; P:negative regulation of blood vessel endothelial cell migration; IEA:Ensembl.
GO; GO:0043371; P:negative regulation of CD4-positive, alpha-beta T cell differentiation; IEA:Ensembl.
GO; GO:0032689; P:negative regulation of interferon-gamma production; IEA:Ensembl.
GO; GO:0017055; P:negative regulation of RNA polymerase II transcriptional preinitiation complex assembly; IEA:Ensembl.
GO; GO:0097350; P:neutrophil clearance; IEA:Ensembl.
GO; GO:0002270; P:plasmacytoid dendritic cell activation; IEA:Ensembl.
GO; GO:0042104; P:positive regulation of activated T cell proliferation; IEA:Ensembl.
GO; GO:0043280; P:positive regulation of cysteine-type endopeptidase activity involved in apoptotic process; IEA:Ensembl.
GO; GO:0007204; P:positive regulation of cytosolic calcium ion concentration; IEA:Ensembl.
GO; GO:2001200; P:positive regulation of dendritic cell differentiation; IEA:Ensembl.
GO; GO:0043388; P:positive regulation of DNA binding; IEA:Ensembl.
GO; GO:0070374; P:positive regulation of ERK1 and ERK2 cascade; IEA:Ensembl.
GO; GO:0045819; P:positive regulation of glycogen catabolic process; IEA:Ensembl.
GO; GO:0032727; P:positive regulation of interferon-alpha production; IEA:Ensembl.
GO; GO:0032728; P:positive regulation of interferon-beta production; IEA:Ensembl.
GO; GO:0050718; P:positive regulation of interleukin-1 beta secretion; IEA:Ensembl.
GO; GO:0032733; P:positive regulation of interleukin-10 production; IEA:Ensembl.
GO; GO:0032735; P:positive regulation of interleukin-12 production; IEA:Ensembl.
GO; GO:2000778; P:positive regulation of interleukin-6 secretion; IEA:Ensembl.
GO; GO:0046330; P:positive regulation of JNK cascade; IEA:Ensembl.
GO; GO:0032425; P:positive regulation of mismatch repair; IEA:Ensembl.
GO; GO:0090026; P:positive regulation of monocyte chemotaxis; IEA:Ensembl.
GO; GO:0045639; P:positive regulation of myeloid cell differentiation; IEA:Ensembl.
GO; GO:1901224; P:positive regulation of NIK/NF-kappaB signaling; IEA:Ensembl.
GO; GO:1903672; P:positive regulation of sprouting angiogenesis; IEA:Ensembl.
GO; GO:0034137; P:positive regulation of toll-like receptor 2 signaling pathway; IEA:Ensembl.
GO; GO:0034145; P:positive regulation of toll-like receptor 4 signaling pathway; IEA:Ensembl.
GO; GO:0045944; P:positive regulation of transcription from RNA polymerase II promoter; IEA:Ensembl.
GO; GO:0032760; P:positive regulation of tumor necrosis factor production; IEA:Ensembl.
GO; GO:0090303; P:positive regulation of wound healing; IEA:Ensembl.
GO; GO:0010506; P:regulation of autophagy; IEA:Ensembl.
GO; GO:2000819; P:regulation of nucleotide-excision repair; IEA:Ensembl.
GO; GO:0032072; P:regulation of restriction endodeoxyribonuclease activity; IEA:Ensembl.
GO; GO:0002840; P:regulation of T cell mediated immune response to tumor cell; IEA:Ensembl.
GO; GO:0002643; P:regulation of tolerance induction; IEA:Ensembl.
GO; GO:0051384; P:response to glucocorticoid; IEA:Ensembl.
GO; GO:0035711; P:T-helper 1 cell activation; IEA:Ensembl.
GO; GO:0045063; P:T-helper 1 cell differentiation; IEA:Ensembl.
GO; GO:1990774; P:tumor necrosis factor secretion; IEA:Ensembl.
GO; GO:0033151; P:V(D)J recombination; IEA:Ensembl.
Gene3D; 1.10.30.10; -; 2.
InterPro; IPR009071; HMG_box_dom.
InterPro; IPR036910; HMG_box_dom_sf.
InterPro; IPR017967; HMG_boxA_CS.
Pfam; PF00505; HMG_box; 1.
Pfam; PF09011; HMG_box_2; 1.
SMART; SM00398; HMG; 2.
SUPFAM; SSF47095; SSF47095; 2.
PROSITE; PS00353; HMG_BOX_1; 1.
PROSITE; PS50118; HMG_BOX_2; 2.
1: Evidence at protein level;
Chromosome; Complete proteome; Cytoplasm; Disulfide bond; DNA-binding;
Immunity; Inflammatory response; Innate immunity; Nucleus; Oxidation;
Reference proteome; Repeat; Secreted.
INIT_MET 1 1 Removed. {ECO:0000250|UniProtKB:P10103}.
CHAIN 2 215 High mobility group protein B1.
/FTId=PRO_0000423460.
DNA_BIND 9 79 HMG box 1. {ECO:0000255|PROSITE-
ProRule:PRU00267}.
DNA_BIND 95 163 HMG box 2. {ECO:0000255|PROSITE-
ProRule:PRU00267}.
REGION 27 43 NLS 1. {ECO:0000250|UniProtKB:P63159}.
REGION 178 184 NLS 2. {ECO:0000250|UniProtKB:P63159}.
REGION 196 210 Involved in intramolecular interaction
with K-3.
REGION 211 215 Involved in interaction with histone H3.
MOTIF 27 43 Nuclear localization signal (NLS) 1.
{ECO:0000250|UniProtKB:P63159}.
MOTIF 178 184 Nuclear localization signal (NLS) 2.
{ECO:0000250|UniProtKB:P63159}.
COMPBIAS 186 215 Asp/Glu-rich (acidic).
SITE 3 3 Involved in intramolecular interaction
with the C-terminal acidic tail.
MOD_RES 23 23 Cysteine sulfonic acid (-SO3H);
alternate.
{ECO:0000250|UniProtKB:P63159}.
MOD_RES 45 45 Cysteine sulfonic acid (-SO3H);
alternate.
{ECO:0000250|UniProtKB:P63159}.
MOD_RES 106 106 Cysteine sulfonic acid (-SO3H).
{ECO:0000250|UniProtKB:P63159}.
DISULFID 23 45 In disulfide HMGB1.
{ECO:0000250|UniProtKB:P63159}.
MUTAGEN 3 3 K->A: Impairs binding to distorted DNA;
when associated with A-12.
{ECO:0000269|PubMed:18241198}.
MUTAGEN 12 12 K->A: Impairs binding to distorted DNA;
when associated with A-3.
{ECO:0000269|PubMed:18241198}.
CONFLICT 214 214 Missing (in Ref. 3; AAD52670).
{ECO:0000305}.
SEQUENCE 215 AA; 24909 MW; 3731F50262DCB1C3 CRC64;
MGKGDPKKPR GKMSSYAFFV QTCREEHKKK HPDASVNFSE FSKKCSERWK TMSSKEKGKF
EDMAKADKLR YEKEMKNYVP PKGETKKKFK DPNAPKRPPS AFFLFCSEFR PKIKGEHPGL
SIGDVAKKLG EMWNNTAADD KQPYEKKAAK LKEKYEKDIA AYRAKGKVDA GKKVVAKAEK
SKKKKEEEED EDEDEEDEED EEEEEEEEED DDDDE


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