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 03-AUG-2022, entry version 145.
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.ENSGALP00000027541; -.
DR PaxDb; Q9YH06; -.
DR Ensembl; ENSGALT00000062837; ENSGALP00000047606; ENSGALG00000042875.
DR Ensembl; ENSGALT00000075072; ENSGALP00000044781; ENSGALG00000042875.
DR Ensembl; ENSGALT00000106579; ENSGALP00000074061; ENSGALG00000042875.
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; GEMWNSK; -.
DR OrthoDB; 1641977at2759; -.
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 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 Gene3D; 1.10.30.10; -; 2.
DR InterPro; IPR009071; HMG_box_dom.
DR InterPro; IPR036910; HMG_box_dom_sf.
DR InterPro; IPR017967; HMG_boxA_CS.
DR InterPro; IPR031076; HMGB1.
DR PANTHER; PTHR48112:SF4; PTHR48112:SF4; 1.
DR Pfam; PF00505; HMG_box; 1.
DR Pfam; PF09011; HMG_box_2; 1.
DR SMART; SM00398; HMG; 2.
DR SUPFAM; SSF47095; SSF47095; 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
