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(-) Description

Title :  SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF THE HMGB2
 
Authors :  J. Kurita, H. Shimahara, M. Yoshida, S. Tate
Date :  19 Feb 03  (Deposition) - 29 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (30x)
Keywords :  Hmg-Box, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Kurita, H. Shimahara, M. Yoshida, S. Tate
Strucutral Comparison Of Two Hmg-Boxes In The Non-Histone Protein Hmg-2 With In The Hmg-1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HIGH MOBILITY GROUP PROTEIN 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-22B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL DOMAIN
    MutationYES
    Organism CommonPIG
    Organism ScientificSUS SCROFA
    Organism Taxid9823
    SynonymHIGH MOBILITY GROUP B2(HMG2) A DOMAIN

 Structural Features

(-) Chains, Units

  
NMR Structure (30x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1J3X)

(-) Sites  (0, 0)

(no "Site" information available for 1J3X)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J3X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J3X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J3X)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HMG_BOX_2PS50118 HMG boxes A and B DNA-binding domains profile.HMGB2_PIG9-79
95-163
  1A:9-77
-
2HMG_BOX_1PS00353 HMG box A DNA-binding domain signature.HMGB2_PIG41-52  1A:41-52

(-) Exons   (0, 0)

(no "Exon" information available for 1J3X)

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:77
 aligned with HMGB2_PIG | P17741 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:77
                                    10        20        30        40        50        60        70       
             HMGB2_PIG    1 MGKGDPNKPRGKMSSYAFFVQTCREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKSDKARYDREMKN 77
               SCOP domains d1j3xa_ A: High mobility group protein 2, HMG2                                SCOP domains
               CATH domains 1j3xA00 A:1-77 DNA Binding (I), subunit A                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------HMG_BOX_2  PDB: A:9-77 UniProt: 9-79                                  PROSITE (1)
                PROSITE (2) ----------------------------------------HMG_BOX_1   ------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------- Transcript
                  1j3x A  1 MGKGDPNKPRGKMSSYAFFVQTSREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKSDKARYDREMKN 77
                                    10        20        30        40        50        60        70       

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J3X)

(-) Gene Ontology  (49, 49)

NMR Structure(hide GO term definitions)
Chain A   (HMGB2_PIG | P17741)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008301    DNA binding, bending    The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    GO:0001158    enhancer sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter.
    GO:0000400    four-way junction DNA binding    Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices.
    GO:0044378    non-sequence-specific DNA binding, bending    The activity of binding selectively and non-covalently to DNA in a sequence-independent manner and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence.
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
    GO:0097100    supercoiled DNA binding    Interacting selectively and non-covalently with supercoiled DNA. For example, during replication and transcription, template DNA is negatively supercoiled in the receding downstream DNA and positively supercoiled in the approaching downstream DNA.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    GO:0032392    DNA geometric change    The process in which a transformation is induced in the geometry of a DNA double helix, resulting in a change in twist, writhe, or both, but with no change in linking number. Includes the unwinding of double-stranded DNA by helicases.
    GO:0051103    DNA ligation involved in DNA repair    The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, that contributes to DNA repair.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0006265    DNA topological change    The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0050829    defense response to Gram-negative bacterium    Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
    GO:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0002437    inflammatory response to antigenic stimulus    An inflammatory response to an antigenic stimulus, which can be include any number of T cell or B cell epitopes.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0008584    male gonad development    The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
    GO:1902042    negative regulation of extrinsic apoptotic signaling pathway via death domain receptors    Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0006334    nucleosome assembly    The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
    GO:0043388    positive regulation of DNA binding    Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045595    regulation of cell differentiation    Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features.
    GO:0050767    regulation of neurogenesis    Any process that modulates the frequency, rate or extent of neurogenesis, the origin and formation of neurons.
    GO:0072091    regulation of stem cell proliferation    Any process that modulates the frequency, rate or extent of stem cell proliferation. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0048545    response to steroid hormone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a steroid hormone stimulus.
    GO:0007289    spermatid nucleus differentiation    The specialization of the spermatid nucleus during the development of a spermatid into a mature male gamete competent for fertilization.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000793    condensed chromosome    A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        HMGB2_PIG | P177411j3c 1j3d

(-) Related Entries Specified in the PDB File

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