Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

High mobility group protein B2

Gene

Hmgb2

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

Multifunctional protein with various roles in different cellular compartments. May act in a redox sensitive manner. In the nucleus is an abundant chromatin-associated non-histone protein involved in transcription, chromatin remodeling and V(D)J recombination and probably other processes (By similarity). Binds DNA with a preference to non-canonical DNA structures such as single-stranded DNA. Can bent DNA and enhance DNA flexibility by looping thus providing a mechanism to promote activities on various gene promoters by enhancing transcription factor binding and/or bringing distant regulatory sequences into close proximity. 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). Proposed to be involved in the innate immune response to nucleic acids by acting as a cytoplasmic promiscuous immunogenic DNA/RNA sensor which cooperates with subsequent discriminative sensing by specific pattern recognition receptors. In the extracellular compartment acts as a chemokine. Promotes proliferation and migration of endothelial cells implicating AGER/RAGE. Has antimicrobial activity in gastrointestinal epithelial tissues. Involved in inflammatory response to antigenic stimulus coupled with proinflammatory activity. May play a role in germ cell differentiation. Involved in modulation of neurogenesis probably by regulation of neural stem proliferation. Involved in articular cartilage surface maintenance implicating LEF1 and the Wnt/beta-catenin pathway (By similarity).By similarity

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 - Biological processi

Chemotaxis, DNA recombination, Immunity, Inflammatory response, Innate immunity, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiR-RNO-211227. Activation of DNA fragmentation factor.

Names & Taxonomyi

Protein namesi
Recommended name:
High mobility group protein B2
Alternative name(s):
High mobility group protein 2
Short name:
HMG-2
Gene namesi
Name:Hmgb2
Synonyms:Hmg2
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componentsi: Chromosome 11, Chromosome 16

Organism-specific databases

RGDi69291. Hmgb2.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotationBy similarity
  • Chromosome By similarity
  • Cytoplasm By similarity
  • Secreted By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Cytoplasm, Nucleus, Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 210209High mobility group protein B2PRO_0000048537Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi23 ↔ 45In disulfide HMGB2By similarity
Modified residuei23 – 231Cysteine derivative; cysteine sulfonic acid (-SO(3)H) in sulfonyl HMGB2; alternateBy similarity
Modified residuei30 – 301N6-acetyllysineBy similarity
Modified residuei45 – 451Cysteine derivative; cysteine sulfonic acid (-SO(3)H) in sulfonyl HMGB2; alternateBy similarity
Modified residuei106 – 1061Cysteine derivative; cysteine sulfonic acid (-SO(3)H) in sulfonyl HMGB2By similarity
Modified residuei114 – 1141N6-acetyllysineBy similarity

Post-translational modificationi

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 in various cellular compartments: 1- fully reduced HMGB2 (HMGB2C23hC45hC106h), 2- disulfide HMGB2 (HMGB2C23-C45C106h) and 3- sulfonyl HMGB2 (HMGB2C23soC45soC106so).By similarity

Keywords - PTMi

Acetylation, Disulfide bond

Proteomic databases

PaxDbiP52925.
PRIDEiP52925.

PTM databases

iPTMnetiP52925.

Expressioni

Gene expression databases

GenevisibleiP52925. RN.

Interactioni

Subunit structurei

Interacts with POU2F2, POU2F1 and POU3F1. Component of the RAG complex composed of core components RAG1 and RAG2, and associated component HMGB1 or HMGB2. Component of the SET complex, composed of at least ANP32A, APEX1, HMGB2, NME1, SET and TREX1. Directly interacts with SET. Interacts with LEF1.By similarity

GO - Molecular functioni

  • nucleosomal histone binding Source: RGD
  • transcription factor binding Source: AgBase

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000039358.

Structurei

3D structure databases

ProteinModelPortaliP52925.
SMRiP52925. Positions 5-166.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni165 – 18016Required for chemotactic activityBy similarityAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi186 – 21025Asp/Glu-rich (acidic)Add
BLAST

Domaini

Both, HMG box 1 and HMG box 2, show antimicrobial activity.By similarity

Sequence similaritiesi

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

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0381. Eukaryota.
COG5648. LUCA.
GeneTreeiENSGT00760000119164.
HOGENOMiHOG000197861.
HOVERGENiHBG009000.
InParanoidiP52925.
KOiK11295.
OMAiIKNDHPG.
OrthoDBiEOG7WHHBQ.
PhylomeDBiP52925.
TreeFamiTF105371.

Family and domain databases

Gene3Di1.10.30.10. 2 hits.
InterProiIPR009071. HMG_box_dom.
IPR017967. HMG_boxA_CS.
IPR031075. HMGB2.
[Graphical view]
PANTHERiPTHR13711:SF217. PTHR13711:SF217. 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.

P52925-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGKGDPNKPR GKMSSYAFFV QTCREEHKKK HPDSSVNFAE FSKKCSERWK
60 70 80 90 100
TMSAKEKSKF EDLAKSDKAR YDREMKNYVP PKGDKKGKKK DPNAPKRPPS
110 120 130 140 150
AFFLFCSEHR PKIKSEHPGL SIGDTAKKLG EMWSEQSAKD KQPYEQKAAK
160 170 180 190 200
LKEKYEKDIA AYRAKGKSEV GKKGPGRPTG SKKKNEPEDE EEEEEEEDDE
210
DEEEEDEDEE
Length:210
Mass (Da):24,159
Last modified:January 23, 2007 - v2
Checksum:i3B5CBAF61415C6F3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D84418 mRNA. Translation: BAA12350.1.
BC078866 mRNA. Translation: AAH78866.1.
BC089854 mRNA. Translation: AAH89854.1.
BC107455 mRNA. Translation: AAI07456.1.
RefSeqiNP_058883.1. NM_017187.2.
XP_001063065.2. XM_001063065.5.
XP_573272.3. XM_573272.5.
UniGeneiRn.218982.
Rn.2874.

Genome annotation databases

EnsembliENSRNOT00000017635; ENSRNOP00000017635; ENSRNOG00000013167.
ENSRNOT00000046874; ENSRNOP00000039358; ENSRNOG00000033321.
GeneIDi29395.
498072.
KEGGirno:29395.
rno:498072.
UCSCiRGD:69291. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D84418 mRNA. Translation: BAA12350.1.
BC078866 mRNA. Translation: AAH78866.1.
BC089854 mRNA. Translation: AAH89854.1.
BC107455 mRNA. Translation: AAI07456.1.
RefSeqiNP_058883.1. NM_017187.2.
XP_001063065.2. XM_001063065.5.
XP_573272.3. XM_573272.5.
UniGeneiRn.218982.
Rn.2874.

3D structure databases

ProteinModelPortaliP52925.
SMRiP52925. Positions 5-166.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000039358.

PTM databases

iPTMnetiP52925.

Proteomic databases

PaxDbiP52925.
PRIDEiP52925.

Protocols and materials databases

DNASUi29395.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000017635; ENSRNOP00000017635; ENSRNOG00000013167.
ENSRNOT00000046874; ENSRNOP00000039358; ENSRNOG00000033321.
GeneIDi29395.
498072.
KEGGirno:29395.
rno:498072.
UCSCiRGD:69291. rat.

Organism-specific databases

CTDi3148.
498072.
RGDi69291. Hmgb2.

Phylogenomic databases

eggNOGiKOG0381. Eukaryota.
COG5648. LUCA.
GeneTreeiENSGT00760000119164.
HOGENOMiHOG000197861.
HOVERGENiHBG009000.
InParanoidiP52925.
KOiK11295.
OMAiIKNDHPG.
OrthoDBiEOG7WHHBQ.
PhylomeDBiP52925.
TreeFamiTF105371.

Enzyme and pathway databases

ReactomeiR-RNO-211227. Activation of DNA fragmentation factor.

Miscellaneous databases

PROiP52925.

Gene expression databases

GenevisibleiP52925. RN.

Family and domain databases

Gene3Di1.10.30.10. 2 hits.
InterProiIPR009071. HMG_box_dom.
IPR017967. HMG_boxA_CS.
IPR031075. HMGB2.
[Graphical view]
PANTHERiPTHR13711:SF217. PTHR13711:SF217. 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. "Rat mRNA for chromosomal protein HMG2, complete cds."
    Yoshida M.
    Submitted (MAY-1996) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: Fischer.
  2. "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].
    Tissue: Spleen, Testis and Thymus.

Entry informationi

Entry nameiHMGB2_RAT
AccessioniPrimary (citable) accession number: P52925
Secondary accession number(s): Q5FVP0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: January 23, 2007
Last modified: June 8, 2016
This is version 132 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, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

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 one 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.