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Protein

High mobility group protein B2

Gene

HMGB2

Organism
Sus scrofa (Pig)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein 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 (PubMed:11275566). 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 similarity1 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

  • DNA binding Source: UniProtKB
  • DNA binding, bending Source: UniProtKB
  • double-stranded DNA binding Source: AgBase
  • drug binding Source: AgBase
  • enhancer sequence-specific DNA binding Source: AgBase
  • four-way junction DNA binding Source: AgBase
  • non-sequence-specific DNA binding, bending Source: AgBase
  • protein domain specific binding Source: AgBase
  • single-stranded DNA binding Source: AgBase
  • supercoiled DNA binding Source: AgBase
  • transcription factor binding Source: AgBase

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

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

Keywords - Ligandi

DNA-binding

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
OrganismiSus scrofa (Pig)
Taxonomic identifieri9823 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaLaurasiatheriaCetartiodactylaSuinaSuidaeSus
Proteomesi
  • UP000008227 Componenti: Unplaced

Subcellular locationi

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

GO - Cellular componenti

  • cell Source: AgBase
  • condensed chromosome Source: UniProtKB
  • cytoplasm Source: UniProtKB
  • extracellular space Source: AgBase
  • nuclear chromatin Source: AgBase
  • nucleus Source: UniProtKB
  • perinuclear region of cytoplasm Source: UniProtKB
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_0000048536Add
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 residuei35 – 351PhosphoserineBy 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, Phosphoprotein

Proteomic databases

PaxDbiP17741.
PeptideAtlasiP17741.

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

Protein-protein interaction databases

STRINGi9823.ENSSSCP00000010363.

Structurei

Secondary structure

1
210
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 83Combined sources
Helixi15 – 2511Combined sources
Helixi28 – 303Combined sources
Helixi38 – 5114Combined sources
Helixi54 – 7017Combined sources
Turni71 – 744Combined sources
Beta strandi92 – 943Combined sources
Helixi102 – 11615Combined sources
Helixi122 – 13514Combined sources
Turni139 – 1413Combined sources
Helixi147 – 1493Combined sources
Helixi152 – 16312Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1J3CNMR-A88-165[»]
1J3DNMR-A89-165[»]
1J3XNMR-A1-77[»]
ProteinModelPortaliP17741.
SMRiP17741. Positions 5-166.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP17741.

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.
HOGENOMiHOG000197861.
HOVERGENiHBG009000.
InParanoidiP17741.
KOiK11295.

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.

P17741-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGKGDPNKPR GKMSSYAFFV QTCREEHKKK HPDSSVNFAE FSKKCSERWK
60 70 80 90 100
TMSAKEKSKF EDMAKSDKAR YDREMKNYVP PKGDKKGKKK DPNAPKRPPS
110 120 130 140 150
AFFLFCSEHR PKIKSEHPGL SIGDTAKKLG EMWSEQSAKD KQPYEQKAAK
160 170 180 190 200
LKEKYEKDIA AYRAKGKGEA GKKGPGRPTG SKKKNEPEDE EEEEEEEEDE
210
DEEEEDEDEE
Length:210
Mass (Da):24,133
Last modified:January 23, 2007 - v2
Checksum:i28FF308D9B341D83
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02895 mRNA. Translation: AAA31051.1.
PIRiA34719.
RefSeqiNP_999228.1. NM_214063.1.
UniGeneiSsc.226.

Genome annotation databases

GeneIDi397130.
KEGGissc:397130.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02895 mRNA. Translation: AAA31051.1.
PIRiA34719.
RefSeqiNP_999228.1. NM_214063.1.
UniGeneiSsc.226.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1J3CNMR-A88-165[»]
1J3DNMR-A89-165[»]
1J3XNMR-A1-77[»]
ProteinModelPortaliP17741.
SMRiP17741. Positions 5-166.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9823.ENSSSCP00000010363.

Proteomic databases

PaxDbiP17741.
PeptideAtlasiP17741.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi397130.
KEGGissc:397130.

Organism-specific databases

CTDi3148.

Phylogenomic databases

eggNOGiKOG0381. Eukaryota.
COG5648. LUCA.
HOGENOMiHOG000197861.
HOVERGENiHBG009000.
InParanoidiP17741.
KOiK11295.

Miscellaneous databases

EvolutionaryTraceiP17741.

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

  1. "Primary structure of non-histone chromosomal protein HMG2 revealed by the nucleotide sequence."
    Shirakawa H., Tsuda K., Yoshida M.
    Biochemistry 29:4419-4423(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Thymus.
  2. "HMG box A in HMG2 protein functions as a mediator of DNA structural alteration together with box B."
    Nakamura Y., Yoshioka K., Shirakawa H., Yoshida M.
    J. Biochem. 129:643-651(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiHMGB2_PIG
AccessioniPrimary (citable) accession number: P17741
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: January 23, 2007
Last modified: July 6, 2016
This is version 122 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.