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(-) Description

Title :  NMR STRUCTURE OF THE CAD DOMAIN OF CASPASE-ACTIVATED DNASE
 
Authors :  T. Yamazaki, K. Uegaki
Date :  02 Aug 99  (Deposition) - 16 Feb 00  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Alpha-Beta Roll, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Uegaki, T. Otomo, H. Sakahira, M. Shimizu, N. Yumoto, Y. Kyogoku, S. Nagata, T. Yamazaki
Structure Of The Cad Domain Of Caspase-Activated Dnase And Interaction With The Cad Domain Of Its Inhibitor.
J. Mol. Biol. V. 297 1121 2000
PubMed-ID: 10764577  |  Reference-DOI: 10.1006/JMBI.2000.3643
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CASPASE-ACTIVATED DNASE
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentN-TERMINAL DOMAIN, RESIDUES 1-87
    MutationYES
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymDNASE INHIBITED BY DNA FRAGMENTATION FACTOR

 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 1C9F)

(-) Sites  (0, 0)

(no "Site" information available for 1C9F)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1C9F)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1C9F)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CIDE_NPS51135 CIDE-N domain profile.DFFB_MOUSE7-83  1A:7-83

(-) Exons   (0, 0)

(no "Exon" information available for 1C9F)

(-) 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:87
 aligned with DFFB_MOUSE | O54788 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:87
                                    10        20        30        40        50        60        70        80       
            DFFB_MOUSE    1 MCAVLRQPKCVKLRALHSACKFGVAARSCQELLRKGCVRFQLPMPGSRLCLYEDGTEVTDDCFPGLPNDAELLLLTAGETWHGYVSD 87
               SCOP domains d1c9fa_ A: Caspase-activated DNase (CAD), DFF40, N-terminal domain                      SCOP domains
               CATH domains 1c9fA00 A:1-87  [code=3.10.20.10, no name defined]                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeee.......eeee.hhhhhhhhhhhhh.......eeee..................eeeeee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------CIDE_N  PDB: A:7-83 UniProt: 7-83                                            ---- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                  1c9f A  1 MCAVLRQPKCVKLRALHSACKFGVAARSCQELLRKGCVRFQLPMPGSRLCLYEDGTEVTDDCFPGLPNDAELLLLTAGETWHGYVSD 87
                                    10        20        30        40        50        60        70        80       

   Legend:   → Mismatch (orange background)
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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
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1C9F)

(-) Gene Ontology  (15, 15)

NMR Structure(hide GO term definitions)
Chain A   (DFFB_MOUSE | O54788)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004536    deoxyribonuclease activity    Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    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:0006309    apoptotic DNA fragmentation    The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments.
    GO:0030263    apoptotic chromosome condensation    The compaction of chromatin during apoptosis.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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

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        DFFB_MOUSE | O547881f2r 1v0d

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