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(-) Description

Title :  TUMOR SUPPRESSOR P15(INK4B) STRUCTURE BY COMPARATIVE MODELING AND NMR DATA
 
Authors :  C. Yuan, L. Ji, T. L. Selby, I. J. L. Byeon, M. D. Tsai
Date :  29 Oct 99  (Deposition) - 28 Jul 00  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Helix-Turn-Helix, Ankyrin Repeat, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Yuan, J. Li, T. L. Selby, I. J. Byeon, M. D. Tsai
Tumor Suppressor Ink4: Comparisons Of Conformational Properties Between P16(Ink4A) And P18(Ink4C).
J. Mol. Biol. V. 294 201 1999
PubMed-ID: 10556039  |  Reference-DOI: 10.1006/JMBI.1999.3231
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYCLIN-DEPENDENT KINASE 4 INHIBITOR B
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPGEX-2T
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  
NMR Structure (10x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1D9S)

(-) Sites  (0, 0)

(no "Site" information available for 1D9S)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1D9S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1D9S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1D9S)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ANK_REP_REGIONPS50297 Ankyrin repeat region circular profile.CDN2B_MOUSE5-130  1A:5-130
2ANK_REPEATPS50088 Ankyrin repeat profile.CDN2B_MOUSE5-37  1A:5-37

(-) Exons   (0, 0)

(no "Exon" information available for 1D9S)

(-) 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:136
 aligned with CDN2B_MOUSE | P55271 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:136
                                  1                                                                                                                                 
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124      
          CDN2B_MOUSE     - ------MLGGSSDAGLATAAARGQVETVRQLLEAGADPNALNRFGRRPIQVMMMGSAQVAELLLLHGAEPNCADPATLTRPVHDAAREGFLDTLVVLHRAGARLDVCDAWGRLPVDLAEEQGHRDIARYLHAATGD 130
               SCOP domains d1d9sa_ A: Tumor suppressor p15(ink4b)                                                                                                   SCOP domains
               CATH domains 1d9sA00 A:-5-130  [code=1.25.40.20, no name defined]                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhh.hhhhhhhhhhh.....................hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------ANK_REPEAT  PDB: A:5-37          --------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----------ANK_REP_REGION  PDB: A:5-130 UniProt: 5-130                                                                                    PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d9s A  -5 GSPGIHMLGGSSDAGLATAAARGQVETVRQLLEAGADPNALNRFGRRPIQVMMMGSAQVAELLLLHGAEPNCADPATLTRPVHDAAREGFLDTLVVLHRAGARLDVCDAWGRLPVDLAEEQGHRDIARYLHAATGD 130
                                     4        14        24        34        44        54        64        74        84        94       104       114       124      

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 1D9S)

(-) Gene Ontology  (20, 20)

NMR Structure(hide GO term definitions)
Chain A   (CDN2B_MOUSE | P55271)
molecular function
    GO:0004861    cyclin-dependent protein serine/threonine kinase inhibitor activity    Stops, prevents or reduces the activity of a cyclin-dependent protein serine/threonine kinase.
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
biological process
    GO:0000086    G2/M transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0031668    cellular response to extracellular stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an extracellular stimulus.
    GO:0031670    cellular response to nutrient    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus.
    GO:0030219    megakaryocyte differentiation    The process in which a myeloid precursor cell acquires specializes features of a megakaryocyte.
    GO:0007093    mitotic cell cycle checkpoint    A cell cycle checkpoint that ensures accurate chromosome replication and segregation by preventing progression through a mitotic cell cycle until conditions are suitable for the cell to proceed to the next stage.
    GO:2000134    negative regulation of G1/S transition of mitotic cell cycle    Any cell cycle regulatory process that prevents the commitment of a cell from G1 to S phase of the mitotic cell cycle.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0050680    negative regulation of epithelial cell proliferation    Any process that stops, prevents or reduces the rate or extent of epithelial cell proliferation.
    GO:0042326    negative regulation of phosphorylation    Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.
    GO:0071901    negative regulation of protein serine/threonine kinase activity    Any process that decreases the rate, frequency, or extent of protein serine/threonine kinase activity.
    GO:0030511    positive regulation of transforming growth factor beta receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of TGF-beta receptor signaling pathway activity.
    GO:0000079    regulation of cyclin-dependent protein serine/threonine kinase activity    Any process that modulates the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity.
    GO:0048536    spleen development    The process whose specific outcome is the progression of the spleen over time, from its formation to the mature structure. The spleen is a large vascular lymphatic organ composed of white and red pulp, involved both in hemopoietic and immune system functions.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

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