High mobility group protein B1 - Rattus norvegicus (Rat)

Contribute

Send feedback

Read comments (?) or add your own

P63159 (HMGB1_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified November 16, 2011. Version 80. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

text xml rdf/xml gff fasta

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
High mobility group protein B1

Alternative name(s):
Amphoterin
Heparin-binding protein p30
High mobility group protein 1
Short name=HMG-1

Gene names

Name:	Hmgb1
Synonyms:	Hmg-1, Hmg1

Organism

Rattus norvegicus (Rat)

Taxonomic identifier

10116 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Rattus

Protein attributes

Sequence length	215 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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 By similarity.
Subunit structure	Component of the RAG complex composed of core components RAG1 and RAG2, and associated component HMGB1 or HMGB2 By similarity.
Subcellular location	Nucleus. Cytoplasm. Chromosome. Note: Associated with the plasma membrane of filipodia in process-growing cells, and also deposited into the substrate-attached material.
Sequence similarities	Belongs to the HMGB family. Contains 2 HMG box DNA-binding domains.

Ontologies

Keywords
Cellular component	Chromosome Cytoplasm Nucleus
Domain	Repeat
Ligand	DNA-binding Heparin-binding
PTM	Acetylation Isopeptide bond Phosphoprotein Ubl conjugation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	DNA geometric change Inferred from direct assay. Source: MGI actin cytoskeleton reorganization Inferred from mutant phenotype. Source: RGD cell morphogenesis Inferred from mutant phenotype Ref.3. Source: RGD cellular response to interleukin-1 Inferred from expression pattern. Source: RGD chemotaxis Inferred from direct assay. Source: RGD circadian rhythm Inferred from expression pattern. Source: RGD induction of positive chemotaxis Inferred from direct assay. Source: MGI male-specific defense response to bacterium Inferred from direct assay. Source: RGD myoblast proliferation Inferred from mutant phenotype. Source: RGD negative regulation of DNA replication Inferred from direct assay. Source: RGD neuron projection development Inferred from genetic interaction. Source: UniProtKB positive regulation of mesenchymal cell proliferation Inferred from direct assay. Source: MGI positive regulation of mitotic cell cycle Inferred from direct assay. Source: MGI positive regulation of myeloid cell apoptosis Inferred from direct assay. Source: RGD positive regulation of myoblast differentiation Inferred from mutant phenotype. Source: RGD positive regulation of neuron projection development Inferred from mutant phenotype. Source: RGD positive regulation of smooth muscle cell migration Inferred from mutant phenotype. Source: RGD regulation of inflammatory response Inferred from direct assay. Source: RGD response to drug Inferred from expression pattern. Source: RGD response to glucose stimulus Inferred from expression pattern. Source: RGD response to heat Inferred from expression pattern. Source: RGD response to insulin stimulus Inferred from expression pattern. Source: RGD response to interferon-gamma Inferred from mutant phenotype. Source: RGD response to lipopolysaccharide Inferred from expression pattern. Source: RGD
Cellular component	chromosome Inferred from electronic annotation. Source: UniProtKB-SubCell cytoplasm Inferred from direct assay. Source: RGD extracellular space Inferred from direct assay. Source: RGD nucleus Inferred from direct assay. Source: RGD
Molecular function	5S rRNA binding Inferred from direct assay. Source: RGD DNA binding, bending Inferred from direct assay. Source: RGD RAGE receptor binding Inferred from physical interaction. Source: UniProtKB bent DNA binding Inferred from direct assay. Source: MGI crossed form four-way junction DNA binding Inferred from direct assay. Source: MGI cytokine activity Inferred from direct assay. Source: UniProtKB double-stranded DNA binding Inferred from direct assay. Source: RGD glycolipid binding Inferred from direct assay. Source: RGD heparin binding Inferred from direct assay. Source: RGD open form four-way junction DNA binding Inferred from direct assay. Source: MGI peptide binding Inferred from direct assay. Source: RGD protein dimerization activity Inferred from direct assay. Source: RGD single-stranded DNA binding Inferred from direct assay. Source: RGD transcription factor binding Inferred from direct assay. Source: RGD
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.6

Chain

2 – 215

214

High mobility group protein B1

PRO_0000048530

Regions

DNA binding

9 – 79

HMG box 1

DNA binding

95 – 163

HMG box 2

Compositional bias

186 – 215

Asp/Glu-rich (acidic)

Amino acid modifications

Modified residue

N6-acetyllysine By similarity

Modified residue

N6-acetyllysine By similarity

Modified residue

Phosphoserine By similarity

Modified residue

100

Phosphoserine By similarity

Cross-link

112

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) By similarity

Secondary structure

215

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P63159 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 8A868DE266D552B5
Show »

FASTA

215

24,894

        10         20         30         40         50         60 
MGKGDPKKPR GKMSSYAFFV QTCREEHKKK HPDASVNFSE FSKKCSERWK TMSAKEKGKF 

        70         80         90        100        110        120 
EDMAKADKAR YEREMKTYIP PKGETKKKFK DPNAPKRPPS AFFLFCSEYR PKIKGEHPGL 

       130        140        150        160        170        180 
SIGDVAKKLG EMWNNTAADD KQPYEKKAAK LKEKYEKDIA AYRAKGKPDA AKKGVVKAEK 

       190        200        210 
SKKKKEEEDD EEDEEDEEEE EEEEDEDEEE DDDDE

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequence of rat liver HMG1 cDNA." Paonessa G., Frank R., Cortese R. Nucleic Acids Res. 15:9077-9077(1987) [PubMed: 3684582] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Strain: Sprague-Dawley. Tissue: Liver.
[2]	Bianchi M. Submitted (DEC-1988) to the EMBL/GenBank/DDBJ databases Cited for: SEQUENCE REVISION.
[3]	"30-kDa heparin-binding protein of brain (amphoterin) involved in neurite outgrowth. Amino acid sequence and localization in the filopodia of the advancing plasma membrane." Merenmies J., Pihlaskari R., Laitinen J., Wartiovaara J., Rauvala H. J. Biol. Chem. 266:16722-16729(1991) [PubMed: 1885601] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE.
[4]	"Amphoterin is associated with the development of the kidney." Ito T., Suzuki A., Horimoto N., Imai E., Hori M. Submitted (JUN-2000) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Strain: Sprague-Dawley. Tissue: Kidney.
[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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Kidney, Prostate and Testis.
[6]	"The adhesive and neurite-promoting molecule p30: analysis of the amino-terminal sequence and production of antipeptide antibodies that detect p30 at the surface of neuroblastoma cells and of brain neurons." Rauvala H., Merenmies J., Pihlaskari R., Korkolainen M., Huhtala M.L., Panula P. J. Cell Biol. 107:2293-2305(1988) [PubMed: 2461949] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-21.
[7]	"Structure of the HMG box motif in the B-domain of HMG1." Weir H.M., Kraulis P.J., Hill C.S., Raine A.R.C., Laue E.D., Thomas J.O. EMBO J. 12:1311-1319(1993) [PubMed: 8467791] [Abstract] Cited for: STRUCTURE BY NMR OF 88-165.
[8]	"Structure of the A-domain of HMG1 and its interaction with DNA as studied by heteronuclear three- and four-dimensional NMR spectroscopy." Hardman C.H., Broadhurst R.W., Raine A.R.C., Grasser K.D., Thomas J.O., Laue E.D. Biochemistry 34:16596-16607(1995) [PubMed: 8527432] [Abstract] Cited for: STRUCTURE BY NMR OF 1-84. Strain: Sprague-Dawley.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M64986 mRNA. Translation: AAA40729.1.
Y00463 mRNA. Translation: CAA68526.1.
AF275734 mRNA. Translation: AAF82799.1.
BC061779 mRNA. Translation: AAH61779.1.
BC081839 mRNA. Translation: AAH81839.1.
BC088402 mRNA. Translation: AAH88402.1.

IPI

IPI00555214.

PIR

NSRTH1. A41175.

RefSeq

NP_037095.1. NM_012963.2.

UniGene

Rn.144565.
Rn.15185.
Rn.4121.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1AAB	NMR	-	A	2-84	[»]
1CKT	X-ray	2.50	A	8-77	[»]
1HME	NMR	-	A	89-165	[»]
1HMF	NMR	-	A	89-165	[»]
2GZK	NMR	-	A	82-165	[»]

ProteinModelPortal

P63159.

SMR

P63159. Positions 5-166.

ModBase

Search...

Protein-protein interaction databases

STRING

P63159.

PTM databases

PhosphoSite

P63159.

Proteomic databases

PRIDE

P63159.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

25459.

KEGG

rno:25459.

UCSC

BC061779. rat.

Organism-specific databases

CTD

3146.

RGD

2802. Hmgb1.

Phylogenomic databases

eggNOG

roNOG11154.

GeneTree

ENSGT00560000076717.

HOVERGEN

HBG009000.

InParanoid

P63159.

OrthoDB

EOG4KWJV1.

PhylomeDB

P63159.

Gene expression databases

Genevestigator

P63159.

GermOnline

ENSRNOG00000030351. Rattus norvegicus.

Family and domain databases

InterPro

IPR011989. ARM-like.
IPR017967. HMG_boxA_CS.
IPR000910. HMG_HMG1/HMG2.
IPR000135. HMG_HMG1/HMG2_subgr.
IPR009071. HMG_superfamily.
[Graphical view]

Gene3D

G3DSA:1.25.10.10. ARM-like. 1 hit.
G3DSA:1.10.30.10. HMG-box. 2 hits.

K10802.

Pfam

PF00505. HMG_box. 2 hits.
[Graphical view]

PRINTS

PR00886. HIGHMOBLTY12.

SMART

SM00398. HMG. 2 hits.
[Graphical view]

SUPFAM

SSF47095. HMG-box. 2 hits.

PROSITE

PS00353. HMG_BOX_1. 1 hit.
PS50118. HMG_BOX_2. 2 hits.
[Graphical view]

ProtoNet

Search...

Other

NextBio

606729.

Entry information

Entry name

HMGB1_RAT

Accession

Primary (citable) accession number: P63159
Secondary accession number(s): P07155

Q548R9

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1988
Last sequence update:	January 23, 2007
Last modified:	November 16, 2011
This is version 80 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Amino acid modifications

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

PTM databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents