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Protein

High mobility group protein B1

Gene

Hmgb1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

DNA binding proteins that associates with chromatin and has the ability to bend DNA. Binds preferentially single-stranded DNA. Involved in V(D)J recombination by acting as a cofactor of the RAG complex. Acts by stimulating cleavage and RAG protein binding at the 23 bp spacer of conserved recombination signal sequences (RSS). Heparin-binding protein that has a role in the extension of neurite-type cytoplasmic processes in developing cells.1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi9 – 7971HMG box 1PROSITE-ProRule annotationAdd
BLAST
DNA bindingi95 – 16369HMG box 2PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

DNA-binding, Heparin-binding

Enzyme and pathway databases

ReactomeiREACT_275137. TRAF6 mediated NF-kB activation.
REACT_283225. RIP-mediated NFkB activation via ZBP1.
REACT_299111. Activation of DNA fragmentation factor.
REACT_305279. TAK1 activates NFkB by phosphorylation and activation of IKKs complex.
REACT_342554. Advanced glycosylation endproduct receptor signaling.
REACT_343658. DEx/H-box helicases activate type I IFN and inflammatory cytokines production.

Names & Taxonomyi

Protein namesi
Recommended name:
High mobility group protein B1
Alternative name(s):
High mobility group protein 1
Short name:
HMG-1
Gene namesi
Name:Hmgb1
Synonyms:Hmg-1, Hmg1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Chromosome 5

Organism-specific databases

MGIiMGI:96113. Hmgb1.

Subcellular locationi

  • Nucleus
  • Cytoplasm
  • Chromosome

  • Note: Associated with the plasma membrane of filipodia in process-growing cells, and also deposited into the substrate-attached material.

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11RemovedBy similarity
Chaini2 – 215214High mobility group protein B1PRO_0000048528Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei30 – 301N6-acetyllysine1 Publication
Modified residuei35 – 351PhosphoserineBy similarity
Modified residuei43 – 431N6-acetyllysine1 Publication
Modified residuei90 – 901N6-acetyllysine1 Publication
Modified residuei100 – 1001PhosphoserineBy similarity
Cross-linki112 – 112Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei141 – 1411N6-acetyllysine1 Publication

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP63158.
PaxDbiP63158.
PRIDEiP63158.

PTM databases

PhosphoSiteiP63158.

Expressioni

Gene expression databases

BgeeiP63158.
CleanExiMM_HMGB1.
ExpressionAtlasiP63158. baseline and differential.
GenevisibleiP63158. MM.

Interactioni

Subunit structurei

Component of the RAG complex composed of core components RAG1 and RAG2, and associated component HMGB1 or HMGB2.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
Becn1O885973EBI-6665811,EBI-643716
Havcr2Q8VIM04EBI-6665811,EBI-6665112
POU5F1Q018603EBI-6665811,EBI-475687From a different organism.

Protein-protein interaction databases

BioGridi200322. 1 interaction.
IntActiP63158. 9 interactions.
MINTiMINT-225214.
STRINGi10090.ENSMUSP00000082682.

Structurei

3D structure databases

DisProtiDP00384.
ProteinModelPortaliP63158.
SMRiP63158. Positions 5-166.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi186 – 21530Asp/Glu-rich (acidic)Add
BLAST

Sequence similaritiesi

Belongs to the HMGB family.Curated
Contains 2 HMG box DNA-binding domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG5648.
GeneTreeiENSGT00760000119164.
HOGENOMiHOG000197861.
HOVERGENiHBG009000.
InParanoidiP63158.
KOiK10802.
OMAiAFFFYSQ.
OrthoDBiEOG7WHHBQ.
PhylomeDBiP63158.
TreeFamiTF105371.

Family and domain databases

Gene3Di1.10.30.10. 2 hits.
InterProiIPR009071. HMG_box_dom.
IPR017967. HMG_boxA_CS.
IPR031076. HMGB1.
[Graphical view]
PANTHERiPTHR13711:SF157. PTHR13711:SF157. 1 hit.
PfamiPF00505. HMG_box. 1 hit.
PF09011. HMG_box_2. 1 hit.
[Graphical view]
SMARTiSM00398. HMG. 2 hits.
[Graphical view]
SUPFAMiSSF47095. SSF47095. 2 hits.
PROSITEiPS00353. HMG_BOX_1. 1 hit.
PS50118. HMG_BOX_2. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P63158-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGKGDPKKPR GKMSSYAFFV QTCREEHKKK HPDASVNFSE FSKKCSERWK
60 70 80 90 100
TMSAKEKGKF EDMAKADKAR YEREMKTYIP PKGETKKKFK DPNAPKRPPS
110 120 130 140 150
AFFLFCSEYR PKIKGEHPGL SIGDVAKKLG EMWNNTAADD KQPYEKKAAK
160 170 180 190 200
LKEKYEKDIA AYRAKGKPDA AKKGVVKAEK SKKKKEEEDD EEDEEDEEEE
210
EEEEDEDEEE DDDDE
Length:215
Mass (Da):24,894
Last modified:January 23, 2007 - v2
Checksum:i8A868DE266D552B5
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti179 – 1791E → V in AAA57042 (PubMed:9047378).Curated
Sequence conflicti190 – 1901D → E in CAA56631 (PubMed:7961836).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z11997 mRNA. Translation: CAA78042.1.
X80457 Genomic DNA. Translation: CAA56631.1.
U00431 mRNA. Translation: AAA20508.1.
L38477 mRNA. Translation: AAA57042.1.
BC006586 mRNA. Translation: AAH06586.1.
BC008565 mRNA. Translation: AAH08565.1.
BC083067 mRNA. Translation: AAH83067.1.
BC085090 mRNA. Translation: AAH85090.1.
CCDSiCCDS19883.1.
PIRiI48688.
RefSeqiNP_034569.1. NM_010439.3.
XP_003945388.1. XM_003945339.3.
XP_006504870.1. XM_006504807.2.
UniGeneiMm.207047.
Mm.313345.

Genome annotation databases

EnsembliENSMUST00000085546; ENSMUSP00000082682; ENSMUSG00000066551.
ENSMUST00000093196; ENSMUSP00000106131; ENSMUSG00000066551.
ENSMUST00000110505; ENSMUSP00000106132; ENSMUSG00000066551.
GeneIDi100862258.
15289.
KEGGimmu:100862258.
mmu:15289.
UCSCiuc009apb.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z11997 mRNA. Translation: CAA78042.1.
X80457 Genomic DNA. Translation: CAA56631.1.
U00431 mRNA. Translation: AAA20508.1.
L38477 mRNA. Translation: AAA57042.1.
BC006586 mRNA. Translation: AAH06586.1.
BC008565 mRNA. Translation: AAH08565.1.
BC083067 mRNA. Translation: AAH83067.1.
BC085090 mRNA. Translation: AAH85090.1.
CCDSiCCDS19883.1.
PIRiI48688.
RefSeqiNP_034569.1. NM_010439.3.
XP_003945388.1. XM_003945339.3.
XP_006504870.1. XM_006504807.2.
UniGeneiMm.207047.
Mm.313345.

3D structure databases

DisProtiDP00384.
ProteinModelPortaliP63158.
SMRiP63158. Positions 5-166.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi200322. 1 interaction.
IntActiP63158. 9 interactions.
MINTiMINT-225214.
STRINGi10090.ENSMUSP00000082682.

Chemistry

ChEMBLiCHEMBL2311237.

PTM databases

PhosphoSiteiP63158.

Proteomic databases

MaxQBiP63158.
PaxDbiP63158.
PRIDEiP63158.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000085546; ENSMUSP00000082682; ENSMUSG00000066551.
ENSMUST00000093196; ENSMUSP00000106131; ENSMUSG00000066551.
ENSMUST00000110505; ENSMUSP00000106132; ENSMUSG00000066551.
GeneIDi100862258.
15289.
KEGGimmu:100862258.
mmu:15289.
UCSCiuc009apb.2. mouse.

Organism-specific databases

CTDi3146.
MGIiMGI:96113. Hmgb1.

Phylogenomic databases

eggNOGiCOG5648.
GeneTreeiENSGT00760000119164.
HOGENOMiHOG000197861.
HOVERGENiHBG009000.
InParanoidiP63158.
KOiK10802.
OMAiAFFFYSQ.
OrthoDBiEOG7WHHBQ.
PhylomeDBiP63158.
TreeFamiTF105371.

Enzyme and pathway databases

ReactomeiREACT_275137. TRAF6 mediated NF-kB activation.
REACT_283225. RIP-mediated NFkB activation via ZBP1.
REACT_299111. Activation of DNA fragmentation factor.
REACT_305279. TAK1 activates NFkB by phosphorylation and activation of IKKs complex.
REACT_342554. Advanced glycosylation endproduct receptor signaling.
REACT_343658. DEx/H-box helicases activate type I IFN and inflammatory cytokines production.

Miscellaneous databases

NextBioi287931.
PROiP63158.
SOURCEiSearch...

Gene expression databases

BgeeiP63158.
CleanExiMM_HMGB1.
ExpressionAtlasiP63158. baseline and differential.
GenevisibleiP63158. MM.

Family and domain databases

Gene3Di1.10.30.10. 2 hits.
InterProiIPR009071. HMG_box_dom.
IPR017967. HMG_boxA_CS.
IPR031076. HMGB1.
[Graphical view]
PANTHERiPTHR13711:SF157. PTHR13711:SF157. 1 hit.
PfamiPF00505. HMG_box. 1 hit.
PF09011. HMG_box_2. 1 hit.
[Graphical view]
SMARTiSM00398. HMG. 2 hits.
[Graphical view]
SUPFAMiSSF47095. SSF47095. 2 hits.
PROSITEiPS00353. HMG_BOX_1. 1 hit.
PS50118. HMG_BOX_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Nucleotide sequence of a mouse cDNA encoding the nonhistone chromosomal high mobility group protein-1 (HMG1)."
    Yotov W.V., St Arnaud R.
    Nucleic Acids Res. 20:3516-3516(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: C3H/He.
  2. "The mouse gene coding for high mobility group 1 protein (HMG1)."
    Ferrari S., Ronfani L., Calogero S., Bianchi M.
    J. Biol. Chem. 269:28803-28808(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 129/Sv.
    Tissue: Liver.
  3. "Molecular cloning, expression analysis, and chromosomal localization of mouse Hmg1-containing sequences."
    Pauken C.M., Nagle D.L., Bucan M., Lo C.W.
    Mamm. Genome 5:91-99(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  4. "The conserved lymphokine element-0 in the IL5 promoter binds to a high mobility group-1 protein."
    Marrugo J., Marsh D.G., Ghosh B.
    Mol. Immunol. 33:1119-1125(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: AKR/J.
  5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  6. Lubec G., Kang S.U.
    Submitted (APR-2007) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 31-43 AND 113-127, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: C57BL/6.
    Tissue: Brain.
  7. "Stimulation of V(D)J cleavage by high mobility group proteins."
    van Gent D.C., Hiom K., Paull T.T., Gellert M.
    EMBO J. 16:2665-2670(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, IDENTIFICATION IN THE RAG COMPLEX.
  8. "SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways."
    Park J., Chen Y., Tishkoff D.X., Peng C., Tan M., Dai L., Xie Z., Zhang Y., Zwaans B.M., Skinner M.E., Lombard D.B., Zhao Y.
    Mol. Cell 50:919-930(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-30; LYS-43; LYS-90 AND LYS-141, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Embryonic fibroblast.

Entry informationi

Entry nameiHMGB1_MOUSE
AccessioniPrimary (citable) accession number: P63158
Secondary accession number(s): P07155, P27109, P27428
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: January 23, 2007
Last modified: July 22, 2015
This is version 113 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.