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(-) Description

Title :  SOLUTION STRUCTURE OF 1-112 FRAGMENT OF HUMAN PROGRAMMED CELL DEATH 5 PROTEIN
 
Authors :  Y. Feng, H. Yao, D. Liu, J. Wang
Date :  07 Jul 08  (Deposition) - 16 Jun 09  (Release) - 16 Jun 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Pdcd5, Apoptosis, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Yao, L. Xu, Y. Feng, D. Liu, Y. Chen, J. Wang
Structure-Function Correlation Of Human Programmed Cell Death 5 Protein.
Arch. Biochem. Biophys. V. 486 141 2009
PubMed-ID: 19358820  |  Reference-DOI: 10.1016/J.ABB.2009.03.018
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROGRAMMED CELL DEATH PROTEIN 5
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET-3D-HR52
    FragmentUNP RESIDUES 2-112
    GenePDCD5, TFAR19
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTF-1 CELL APOPTOSIS-RELATED PROTEIN 19, PROTEIN TFAR19

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2K6B)

(-) Sites  (0, 0)

(no "Site" information available for 2K6B)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2K6B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2K6B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 2K6B)

(-) 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    
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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:113
 aligned with PDCD5_HUMAN | O14737 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:113
                             1                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109   
          PDCD5_HUMAN     - -MADEELEALRRQRLAELQAKHGDPGDAAQQEAKHREAEMRNSILAQVLDQSARARLSNLALVKPEKTKAVENYLIQMARYGQLSEKVSEQGLIEILKKVSQQTEKTTTVKFN 112
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------dsDNA_bind-2k6bA01 A:9-112                                                                               Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2k6b A   0 GSADEELEALRRQRLAELQAKHGDPGDAAQQEAKHREAEMRNSILAQVLDQSARARLSNLALVKPEKTKAVENYLIQMARYGQLSEKVSEQGLIEILKKVSQQTEKTTTVKFN 112
                                     9        19        29        39        49        59        69        79        89        99       109   

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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  (0, 0)

(no "SCOP Domain" information available for 2K6B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2K6B)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (17, 17)

NMR Structure(hide GO term definitions)
Chain A   (PDCD5_HUMAN | O14737)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0010698    acetyltransferase activator activity    Binds to and increases the activity of an acetyltransferase, an enzyme which catalyzes the transfer of an acetyl group to an acceptor molecule.
    GO:0048487    beta-tubulin binding    Interacting selectively and non-covalently with the microtubule constituent protein beta-tubulin.
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0071560    cellular response to transforming growth factor beta 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 a transforming growth factor beta stimulus.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:1903645    negative regulation of chaperone-mediated protein folding    Any process that stops, prevents or reduces the frequency, rate or extent of chaperone-mediated protein folding.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0043280    positive regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that activates or increases the activity of a cysteine-type endopeptidase involved in the apoptotic process.
    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:1903638    positive regulation of protein import into mitochondrial outer membrane    Any process that activates or increases the frequency, rate or extent of protein import into mitochondrial outer membrane.
    GO:0090200    positive regulation of release of cytochrome c from mitochondria    Any process that increases the rate, frequency or extent of release of cytochrome c from mitochondria, the process in which cytochrome c is enabled to move from the mitochondrial intermembrane space into the cytosol, which is an early step in apoptosis and leads to caspase activation.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        PDCD5_HUMAN | O147371yyb 2cru

(-) Related Entries Specified in the PDB File

1yyb SOLUTION STRUCTURE OF 1-26 FRAGMENT OF HUMAN PROGRAMMED CELL DEATH 5 PROTEIN