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Database: UniProt
Entry: HMGB1_CHICK
LinkDB: HMGB1_CHICK
Original site: HMGB1_CHICK 
ID   HMGB1_CHICK             Reviewed;         215 AA.
AC   Q9YH06; H9BNX0; Q9PUK9;
DT   18-SEP-2013, integrated into UniProtKB/Swiss-Prot.
DT   01-MAY-1999, sequence version 1.
DT   24-JAN-2024, entry version 150.
DE   RecName: Full=High mobility group protein B1;
DE   AltName: Full=High mobility group protein 1;
DE            Short=HMG-1;
GN   Name=HMGB1; Synonyms=HMG1; ORFNames=RCJMB04_15a21;
OS   Gallus gallus (Chicken).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
OC   Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes; Phasianidae;
OC   Phasianinae; Gallus.
OX   NCBI_TaxID=9031;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RC   TISSUE=B-cell;
RX   PubMed=9931456; DOI=10.1016/s0378-1119(98)00542-3;
RA   Lee K.B., Brooks D.J., Thomas J.O.;
RT   "Selection of a cDNA clone for chicken high-mobility-group 1 (HMG1) protein
RT   through its unusually conserved 3'-untranslated region, and improved
RT   expression of recombinant HMG1 in Escherichia coli.";
RL   Gene 225:97-105(1998).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=CB; TISSUE=Bursa of Fabricius;
RX   PubMed=15642098; DOI=10.1186/gb-2004-6-1-r6;
RA   Caldwell R.B., Kierzek A.M., Arakawa H., Bezzubov Y., Zaim J., Fiedler P.,
RA   Kutter S., Blagodatski A., Kostovska D., Koter M., Plachy J., Carninci P.,
RA   Hayashizaki Y., Buerstedde J.-M.;
RT   "Full-length cDNAs from chicken bursal lymphocytes to facilitate gene
RT   function analysis.";
RL   Genome Biol. 6:R6.1-R6.9(2005).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=10978508; DOI=10.1016/s0167-4781(00)00164-0;
RA   Lum H.K., Lee K.D., Yu G.;
RT   "The chicken genome contains no HMG1 retropseudogenes but a functional HMG1
RT   gene with long introns.";
RL   Biochim. Biophys. Acta 1493:64-72(2000).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Red jungle fowl;
RX   PubMed=15592404; DOI=10.1038/nature03154;
RA   Hillier L.W., Miller W., Birney E., Warren W., Hardison R.C., Ponting C.P.,
RA   Bork P., Burt D.W., Groenen M.A.M., Delany M.E., Dodgson J.B.,
RA   Chinwalla A.T., Cliften P.F., Clifton S.W., Delehaunty K.D., Fronick C.,
RA   Fulton R.S., Graves T.A., Kremitzki C., Layman D., Magrini V.,
RA   McPherson J.D., Miner T.L., Minx P., Nash W.E., Nhan M.N., Nelson J.O.,
RA   Oddy L.G., Pohl C.S., Randall-Maher J., Smith S.M., Wallis J.W.,
RA   Yang S.-P., Romanov M.N., Rondelli C.M., Paton B., Smith J., Morrice D.,
RA   Daniels L., Tempest H.G., Robertson L., Masabanda J.S., Griffin D.K.,
RA   Vignal A., Fillon V., Jacobbson L., Kerje S., Andersson L.,
RA   Crooijmans R.P., Aerts J., van der Poel J.J., Ellegren H., Caldwell R.B.,
RA   Hubbard S.J., Grafham D.V., Kierzek A.M., McLaren S.R., Overton I.M.,
RA   Arakawa H., Beattie K.J., Bezzubov Y., Boardman P.E., Bonfield J.K.,
RA   Croning M.D.R., Davies R.M., Francis M.D., Humphray S.J., Scott C.E.,
RA   Taylor R.G., Tickle C., Brown W.R.A., Rogers J., Buerstedde J.-M.,
RA   Wilson S.A., Stubbs L., Ovcharenko I., Gordon L., Lucas S., Miller M.M.,
RA   Inoko H., Shiina T., Kaufman J., Salomonsen J., Skjoedt K., Wong G.K.-S.,
RA   Wang J., Liu B., Wang J., Yu J., Yang H., Nefedov M., Koriabine M.,
RA   Dejong P.J., Goodstadt L., Webber C., Dickens N.J., Letunic I., Suyama M.,
RA   Torrents D., von Mering C., Zdobnov E.M., Makova K., Nekrutenko A.,
RA   Elnitski L., Eswara P., King D.C., Yang S.-P., Tyekucheva S.,
RA   Radakrishnan A., Harris R.S., Chiaromonte F., Taylor J., He J.,
RA   Rijnkels M., Griffiths-Jones S., Ureta-Vidal A., Hoffman M.M., Severin J.,
RA   Searle S.M.J., Law A.S., Speed D., Waddington D., Cheng Z., Tuzun E.,
RA   Eichler E., Bao Z., Flicek P., Shteynberg D.D., Brent M.R., Bye J.M.,
RA   Huckle E.J., Chatterji S., Dewey C., Pachter L., Kouranov A.,
RA   Mourelatos Z., Hatzigeorgiou A.G., Paterson A.H., Ivarie R., Brandstrom M.,
RA   Axelsson E., Backstrom N., Berlin S., Webster M.T., Pourquie O.,
RA   Reymond A., Ucla C., Antonarakis S.E., Long M., Emerson J.J., Betran E.,
RA   Dupanloup I., Kaessmann H., Hinrichs A.S., Bejerano G., Furey T.S.,
RA   Harte R.A., Raney B., Siepel A., Kent W.J., Haussler D., Eyras E.,
RA   Castelo R., Abril J.F., Castellano S., Camara F., Parra G., Guigo R.,
RA   Bourque G., Tesler G., Pevzner P.A., Smit A., Fulton L.A., Mardis E.R.,
RA   Wilson R.K.;
RT   "Sequence and comparative analysis of the chicken genome provide unique
RT   perspectives on vertebrate evolution.";
RL   Nature 432:695-716(2004).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [MRNA] OF 1-185.
RA   Sawant P.M., Dhama K., Wani M.Y., Upamanyu V., Singh S.D., Somvanshi R.,
RA   Kumar P., Bisla S.R., Chaudhary D., Bassareddi M.;
RL   Submitted (NOV-2011) to the EMBL/GenBank/DDBJ databases.
RN   [6]
RP   DOMAIN, AND SUBCELLULAR LOCATION.
RX   PubMed=19102706; DOI=10.1021/bi8013449;
RA   Kawase T., Sato K., Ueda T., Yoshida M.;
RT   "Distinct domains in HMGB1 are involved in specific intramolecular and
RT   nucleosomal interactions.";
RL   Biochemistry 47:13991-13996(2008).
RN   [7]
RP   MUTAGENESIS OF LYS-3 AND LYS-12.
RX   PubMed=18241198; DOI=10.1042/bj20071613;
RA   Assenberg R., Webb M., Connolly E., Stott K., Watson M., Hobbs J.,
RA   Thomas J.O.;
RT   "A critical role in structure-specific DNA binding for the acetylatable
RT   lysine residues in HMGB1.";
RL   Biochem. J. 411:553-561(2008).
CC   -!- FUNCTION: Multifunctional redox sensitive protein with various roles in
CC       different cellular compartments. Nuclear functions are attributed to
CC       fully reduced HGMB1. Associates with chromatin and binds DNA with a
CC       preference to non-canonical DNA structures such as single-stranded DNA,
CC       DNA-containing cruciforms or bent structures, supercoiled DNA and ZDNA.
CC       Can bent DNA and enhance DNA flexibility by looping thus providing a
CC       mechanism to promote activities on various gene promoters. Can
CC       restructure the canonical nucleosome. Proposed to be an universal
CC       biosensor for nucleic acids. May promote inflammatory response to
CC       sterile and infectious signals and may be involved in the coordination
CC       and integration of innate and adaptive immune responses. In the
CC       cytoplasm may function as sensor and/or chaperone for immunogenic
CC       nucleic acids, and mediate autophagy. May act as danger associated
CC       molecular pattern (DAMP) molecule that amplifies immune responses
CC       during tissue injury. {ECO:0000250|UniProtKB:P09429,
CC       ECO:0000250|UniProtKB:P63158, ECO:0000250|UniProtKB:P63159}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00267,
CC       ECO:0000305|PubMed:19102706}. Chromosome {ECO:0000305|PubMed:19102706}.
CC       Cytoplasm {ECO:0000305}. Secreted {ECO:0000305}.
CC   -!- DOMAIN: The acidic C-terminal domain forms a flexible structure which
CC       can reversibly interact intramolecularily with the HMG boxes and
CC       modulate binding to DNA and other proteins; may involve Lys-3 and
CC       histone H3 'Lys-37' and 'Lys-38'. {ECO:0000250|UniProtKB:P09429,
CC       ECO:0000250|UniProtKB:P63159, ECO:0000269|PubMed:19102706}.
CC   -!- PTM: Reduction/oxidation of cysteine residues Cys-23, Cys-45 and Cys-
CC       106 and a possible intramolecular disulfide bond involving Cys-23 and
CC       Cys-45 give rise to different redox forms with specific functional
CC       activities: 1- fully reduced HMGB1 (HMGB1C23hC45hC106h), 2- disulfide
CC       HMGB1 (HMGB1C23-C45C106h) and 3- sulfonyl HMGB1
CC       (HMGB1C23soC45soC106so). {ECO:0000250|UniProtKB:P09429}.
CC   -!- SIMILARITY: Belongs to the HMGB family. {ECO:0000305}.
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DR   EMBL; Y17968; CAA76978.1; -; mRNA.
DR   EMBL; AJ851648; CAH65282.1; -; mRNA.
DR   EMBL; AF178849; AAD52670.1; -; Genomic_DNA.
DR   EMBL; AADN03000868; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; AADN03001640; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; JQ040530; AFD33645.1; -; mRNA.
DR   RefSeq; NP_990233.1; NM_204902.2.
DR   RefSeq; XP_015133153.1; XM_015277667.1.
DR   RefSeq; XP_015133156.1; XM_015277670.1.
DR   AlphaFoldDB; Q9YH06; -.
DR   SMR; Q9YH06; -.
DR   STRING; 9031.ENSGALP00000074061; -.
DR   PaxDb; 9031-ENSGALP00000027541; -.
DR   Ensembl; ENSGALT00000106579; ENSGALP00000074061; ENSGALG00000042875.
DR   Ensembl; ENSGALT00010016643.1; ENSGALP00010009408.1; ENSGALG00010007011.1.
DR   Ensembl; ENSGALT00015040483; ENSGALP00015023696; ENSGALG00015016593.
DR   GeneID; 395724; -.
DR   KEGG; gga:395724; -.
DR   CTD; 3146; -.
DR   VEuPathDB; HostDB:geneid_395724; -.
DR   eggNOG; KOG0381; Eukaryota.
DR   GeneTree; ENSGT00950000183120; -.
DR   HOGENOM; CLU_082854_0_0_1; -.
DR   InParanoid; Q9YH06; -.
DR   OMA; PHSANEV; -.
DR   PhylomeDB; Q9YH06; -.
DR   TreeFam; TF105371; -.
DR   Reactome; R-GGA-140342; Apoptosis induced DNA fragmentation.
DR   Reactome; R-GGA-5620971; Pyroptosis.
DR   Reactome; R-GGA-5686938; Regulation of TLR by endogenous ligand.
DR   Reactome; R-GGA-6798695; Neutrophil degranulation.
DR   PRO; PR:Q9YH06; -.
DR   Proteomes; UP000000539; Chromosome 1.
DR   Bgee; ENSGALG00000042875; Expressed in spermatid and 14 other cell types or tissues.
DR   GO; GO:0005694; C:chromosome; IEA:UniProtKB-SubCell.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0005576; C:extracellular region; IEA:UniProtKB-SubCell.
DR   GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR   GO; GO:0000405; F:bubble DNA binding; IDA:AgBase.
DR   GO; GO:0008301; F:DNA binding, bending; IDA:AgBase.
DR   GO; GO:0000400; F:four-way junction DNA binding; IDA:AgBase.
DR   GO; GO:0044378; F:non-sequence-specific DNA binding, bending; ISS:AgBase.
DR   GO; GO:0097100; F:supercoiled DNA binding; IDA:AgBase.
DR   GO; GO:0032392; P:DNA geometric change; IDA:AgBase.
DR   GO; GO:0006954; P:inflammatory response; IEA:UniProtKB-KW.
DR   GO; GO:0045087; P:innate immune response; IEA:UniProtKB-KW.
DR   GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR   CDD; cd21978; HMG-box_HMGB_rpt1; 1.
DR   CDD; cd21979; HMG-box_HMGB_rpt2; 1.
DR   Gene3D; 1.10.30.10; High mobility group box domain; 2.
DR   InterPro; IPR009071; HMG_box_dom.
DR   InterPro; IPR036910; HMG_box_dom_sf.
DR   InterPro; IPR017967; HMG_boxA_CS.
DR   PANTHER; PTHR48112:SF12; HIGH MOBILITY GROUP PROTEIN B1; 1.
DR   PANTHER; PTHR48112; HIGH MOBILITY GROUP PROTEIN DSP1; 1.
DR   Pfam; PF00505; HMG_box; 1.
DR   Pfam; PF09011; HMG_box_2; 1.
DR   PRINTS; PR00886; HIGHMOBLTY12.
DR   SMART; SM00398; HMG; 2.
DR   SUPFAM; SSF47095; HMG-box; 2.
DR   PROSITE; PS00353; HMG_BOX_1; 1.
DR   PROSITE; PS50118; HMG_BOX_2; 2.
PE   1: Evidence at protein level;
KW   Chromosome; Cytoplasm; Disulfide bond; DNA-binding; Immunity;
KW   Inflammatory response; Innate immunity; Nucleus; Oxidation;
KW   Reference proteome; Repeat; Secreted.
FT   INIT_MET        1
FT                   /note="Removed"
FT                   /evidence="ECO:0000250|UniProtKB:P10103"
FT   CHAIN           2..215
FT                   /note="High mobility group protein B1"
FT                   /id="PRO_0000423460"
FT   DNA_BIND        9..79
FT                   /note="HMG box 1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00267"
FT   DNA_BIND        95..163
FT                   /note="HMG box 2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00267"
FT   REGION          27..43
FT                   /note="NLS 1"
FT                   /evidence="ECO:0000250|UniProtKB:P63159"
FT   REGION          75..95
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          166..215
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          178..184
FT                   /note="NLS 2"
FT                   /evidence="ECO:0000250|UniProtKB:P63159"
FT   REGION          196..210
FT                   /note="Involved in intramolecular interaction with K-3"
FT   REGION          211..215
FT                   /note="Involved in interaction with histone H3"
FT   MOTIF           27..43
FT                   /note="Nuclear localization signal (NLS) 1"
FT                   /evidence="ECO:0000250|UniProtKB:P63159"
FT   MOTIF           178..184
FT                   /note="Nuclear localization signal (NLS) 2"
FT                   /evidence="ECO:0000250|UniProtKB:P63159"
FT   COMPBIAS        75..94
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        166..187
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        188..215
FT                   /note="Acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   SITE            3
FT                   /note="Involved in intramolecular interaction with the C-
FT                   terminal acidic tail"
FT   MOD_RES         23
FT                   /note="Cysteine sulfonic acid (-SO3H); alternate"
FT                   /evidence="ECO:0000250|UniProtKB:P63159"
FT   MOD_RES         45
FT                   /note="Cysteine sulfonic acid (-SO3H); alternate"
FT                   /evidence="ECO:0000250|UniProtKB:P63159"
FT   MOD_RES         106
FT                   /note="Cysteine sulfonic acid (-SO3H)"
FT                   /evidence="ECO:0000250|UniProtKB:P63159"
FT   DISULFID        23..45
FT                   /note="In disulfide HMGB1"
FT                   /evidence="ECO:0000250|UniProtKB:P63159"
FT   MUTAGEN         3
FT                   /note="K->A: Impairs binding to distorted DNA; when
FT                   associated with A-12."
FT                   /evidence="ECO:0000269|PubMed:18241198"
FT   MUTAGEN         12
FT                   /note="K->A: Impairs binding to distorted DNA; when
FT                   associated with A-3."
FT                   /evidence="ECO:0000269|PubMed:18241198"
FT   CONFLICT        214
FT                   /note="Missing (in Ref. 3; AAD52670)"
FT                   /evidence="ECO:0000305"
SQ   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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