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Protein

High mobility group protein B2

Gene

HMGB2

Organism
Homo sapiens (Human)
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) (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

  • chemoattractant activity Source: UniProtKB
  • chromatin binding Source: GO_Central
  • damaged DNA binding Source: UniProtKB
  • DNA binding Source: UniProtKB
  • DNA binding, bending Source: UniProtKB
  • double-stranded DNA binding Source: UniProtKB
  • poly(A) RNA binding Source: UniProtKB
  • RAGE receptor binding Source: UniProtKB
  • sequence-specific DNA binding transcription factor activity Source: UniProtKB
  • single-stranded DNA binding Source: UniProtKB
  • transcription regulatory region DNA binding Source: UniProtKB

GO - Biological processi

  • apoptotic DNA fragmentation Source: Reactome
  • apoptotic process Source: Reactome
  • base-excision repair, DNA ligation Source: UniProtKB
  • cell chemotaxis Source: UniProtKB
  • cellular component disassembly involved in execution phase of apoptosis Source: Reactome
  • cellular response to lipopolysaccharide Source: UniProtKB
  • chromatin organization Source: UniProtKB
  • chromatin remodeling Source: GO_Central
  • DNA ligation involved in DNA repair Source: UniProtKB
  • DNA topological change Source: UniProtKB
  • male gonad development Source: Ensembl
  • negative regulation of extrinsic apoptotic signaling pathway via death domain receptors Source: Ensembl
  • negative regulation of transcription, DNA-templated Source: BHF-UCL
  • nucleosome assembly Source: UniProtKB
  • positive chemotaxis Source: GOC
  • positive regulation of DNA binding Source: UniProtKB
  • positive regulation of endothelial cell proliferation Source: UniProtKB
  • positive regulation of erythrocyte differentiation Source: UniProtKB
  • positive regulation of megakaryocyte differentiation Source: UniProtKB
  • positive regulation of nuclease activity Source: UniProtKB
  • positive regulation of transcription, DNA-templated Source: UniProtKB
  • positive regulation of transcription from RNA polymerase II promoter Source: UniProtKB
  • programmed cell death Source: Reactome
  • regulation of transcription from RNA polymerase II promoter Source: UniProtKB
  • response to steroid hormone Source: Ensembl
  • spermatid nucleus differentiation Source: Ensembl
  • V(D)J recombination Source: UniProtKB
Complete GO annotation...

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiREACT_13462. 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
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 4

Organism-specific databases

HGNCiHGNC:5000. HMGB2.

Subcellular locationi

GO - Cellular componenti

  • condensed chromosome Source: UniProtKB
  • cytoplasm Source: UniProtKB
  • extracellular space Source: UniProtKB
  • nucleoplasm Source: Reactome
  • nucleus Source: UniProtKB
  • perinuclear region of cytoplasm Source: UniProtKB
  • protein complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA35091.

Polymorphism and mutation databases

BioMutaiHMGB2.
DMDMi123374.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11RemovedBy similarity
Chaini2 – 209208High mobility group protein B2PRO_0000048534Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei30 – 301N6-acetyllysine1 Publication
Modified residuei114 – 1141N6-acetyllysineBy similarity

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiP26583.
PaxDbiP26583.
PeptideAtlasiP26583.
PRIDEiP26583.

PTM databases

PhosphoSiteiP26583.

Miscellaneous databases

PMAP-CutDBP26583.

Expressioni

Gene expression databases

BgeeiP26583.
CleanExiHS_HMGB2.
ExpressionAtlasiP26583. baseline and differential.
GenevisibleiP26583. HS.

Organism-specific databases

HPAiCAB037206.
HPA003506.
HPA053314.

Interactioni

Subunit structurei

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.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
PKNOX1Q96I873EBI-1057009,EBI-10173774

Protein-protein interaction databases

BioGridi109391. 32 interactions.
IntActiP26583. 7 interactions.
MINTiMINT-240190.
STRINGi9606.ENSP00000296503.

Structurei

3D structure databases

ProteinModelPortaliP26583.
SMRiP26583. Positions 1-166.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi186 – 20924Asp/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.
InParanoidiP26583.
KOiK11295.
OMAiIKNDHPG.
OrthoDBiEOG7WHHBQ.
PhylomeDBiP26583.
TreeFamiTF105371.

Family and domain databases

Gene3Di1.10.30.10. 2 hits.
InterProiIPR009071. HMG_box_dom.
IPR017967. HMG_boxA_CS.
[Graphical view]
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.

P26583-1 [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 AYRAKGKSEA GKKGPGRPTG SKKKNEPEDE EEEEEEEDED

EEEEDEDEE
Length:209
Mass (Da):24,034
Last modified:January 23, 2007 - v2
Checksum:i5E65292BC4AD8373
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti163 – 1631R → G in CAA78938 (PubMed:1475204).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M83665 Genomic DNA. Translation: AAA58659.1.
X62534 mRNA. Translation: CAA44395.1.
BT019782 mRNA. Translation: AAV38585.1.
AK311864 mRNA. Translation: BAG34805.1.
CH471056 Genomic DNA. Translation: EAX04758.1.
CH471056 Genomic DNA. Translation: EAX04759.1.
BC001063 mRNA. Translation: AAH01063.1.
BC100019 mRNA. Translation: AAI00020.1.
Z17240 mRNA. Translation: CAA78938.1.
CCDSiCCDS3816.1.
PIRiA42425. NSHUH2.
S30221.
RefSeqiNP_001124160.1. NM_001130688.1.
NP_001124161.1. NM_001130689.1.
NP_002120.1. NM_002129.3.
UniGeneiHs.434953.

Genome annotation databases

EnsembliENST00000296503; ENSP00000296503; ENSG00000164104.
ENST00000438704; ENSP00000404912; ENSG00000164104.
ENST00000446922; ENSP00000393448; ENSG00000164104.
GeneIDi3148.
KEGGihsa:3148.
UCSCiuc003ita.3. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M83665 Genomic DNA. Translation: AAA58659.1.
X62534 mRNA. Translation: CAA44395.1.
BT019782 mRNA. Translation: AAV38585.1.
AK311864 mRNA. Translation: BAG34805.1.
CH471056 Genomic DNA. Translation: EAX04758.1.
CH471056 Genomic DNA. Translation: EAX04759.1.
BC001063 mRNA. Translation: AAH01063.1.
BC100019 mRNA. Translation: AAI00020.1.
Z17240 mRNA. Translation: CAA78938.1.
CCDSiCCDS3816.1.
PIRiA42425. NSHUH2.
S30221.
RefSeqiNP_001124160.1. NM_001130688.1.
NP_001124161.1. NM_001130689.1.
NP_002120.1. NM_002129.3.
UniGeneiHs.434953.

3D structure databases

ProteinModelPortaliP26583.
SMRiP26583. Positions 1-166.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi109391. 32 interactions.
IntActiP26583. 7 interactions.
MINTiMINT-240190.
STRINGi9606.ENSP00000296503.

PTM databases

PhosphoSiteiP26583.

Polymorphism and mutation databases

BioMutaiHMGB2.
DMDMi123374.

Proteomic databases

MaxQBiP26583.
PaxDbiP26583.
PeptideAtlasiP26583.
PRIDEiP26583.

Protocols and materials databases

DNASUi3148.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000296503; ENSP00000296503; ENSG00000164104.
ENST00000438704; ENSP00000404912; ENSG00000164104.
ENST00000446922; ENSP00000393448; ENSG00000164104.
GeneIDi3148.
KEGGihsa:3148.
UCSCiuc003ita.3. human.

Organism-specific databases

CTDi3148.
GeneCardsiGC04M174252.
HGNCiHGNC:5000. HMGB2.
HPAiCAB037206.
HPA003506.
HPA053314.
MIMi163906. gene.
neXtProtiNX_P26583.
PharmGKBiPA35091.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG5648.
GeneTreeiENSGT00760000119164.
HOGENOMiHOG000197861.
HOVERGENiHBG009000.
InParanoidiP26583.
KOiK11295.
OMAiIKNDHPG.
OrthoDBiEOG7WHHBQ.
PhylomeDBiP26583.
TreeFamiTF105371.

Enzyme and pathway databases

ReactomeiREACT_13462. Activation of DNA fragmentation factor.

Miscellaneous databases

ChiTaRSiHMGB2. human.
GeneWikiiHMGB2.
GenomeRNAii3148.
NextBioi12476.
PMAP-CutDBP26583.
PROiP26583.
SOURCEiSearch...

Gene expression databases

BgeeiP26583.
CleanExiHS_HMGB2.
ExpressionAtlasiP26583. baseline and differential.
GenevisibleiP26583. HS.

Family and domain databases

Gene3Di1.10.30.10. 2 hits.
InterProiIPR009071. HMG_box_dom.
IPR017967. HMG_boxA_CS.
[Graphical view]
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. Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "Structure of a gene coding for human HMG2 protein."
    Shirakawa H., Yoshida M.
    J. Biol. Chem. 267:6641-6645(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "Cloning of human full-length CDSs in BD Creator(TM) system donor vector."
    Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A.
    Submitted (OCT-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  4. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Brain.
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. "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: Placenta and Skin.
  7. "A human HMG2 cDNA with a novel 3'-untranslated region."
    Alexandre S., Li W.W., Lee A.S.
    Nucleic Acids Res. 20:6413-6413(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 24-209.
  8. "HMG2 interacts with the nucleosome assembly protein SET and is a target of the cytotoxic T-lymphocyte protease granzyme A."
    Fan Z., Beresford P.J., Zhang D., Lieberman J.
    Mol. Cell. Biol. 22:2810-2820(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE SET COMPLEX, INTERACTION WITH SET.
  9. "Lysine acetylation targets protein complexes and co-regulates major cellular functions."
    Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
    Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-30, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  10. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  11. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  12. "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome."
    Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.
    J. Proteomics 96:253-262(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.

Entry informationi

Entry nameiHMGB2_HUMAN
AccessioniPrimary (citable) accession number: P26583
Secondary accession number(s): B2R4K8, D3DP37, Q5U072
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: January 23, 2007
Last modified: June 24, 2015
This is version 157 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 4
    Human chromosome 4: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. 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.