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(-) Description

Title :  CRYSTAL STRUCTURE OF CASPASE-ACTIVATED DNASE (CAD)
 
Authors :  E. -J. Woo, Y. -G. Kim, M. -S. Kim, W. -D. Han, S. Shin, B. -H. Oh
Date :  26 Mar 04  (Deposition) - 21 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase, Nuclease, Caspase-Activated Dnase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. -J. Woo, Y. -G. Kim, M. -S. Kim, W. -D. Han, S. Shin, H. Robinson, S. -Y. Park, B. -H. Oh
Structural Mechanism For Inactivation And Activation Of Cad/Dff40 In The Apoptotic Pathway
Mol. Cell V. 14 531 2004
PubMed-ID: 15149602  |  Reference-DOI: 10.1016/S1097-2765(04)00258-8

(-) Compounds

Molecule 1 - DNA FRAGMENTATION FACTOR 40 KDA SUBUNIT
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentRESIDUES 1-329
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymDFF-40, CASPASE-ACTIVATED DEOXYRIBONUCLEASE, CASPASE-ACTIVATED DNASECAD

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2PB1Ligand/IonLEAD (II) ION
3ZN1Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PB-1Ligand/IonLEAD (II) ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:229 , CYS A:238 , HIS A:242 , CYS A:307BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREASP A:262 , HIS A:308 , HOH A:2010 , HOH A:2013BINDING SITE FOR RESIDUE MG A 501
3AC3SOFTWARECYS A:197BINDING SITE FOR RESIDUE PB A 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V0D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V0D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V0D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V0D)

(-) Exons   (0, 0)

(no "Exon" information available for 1V0D)

(-) Sequences/Alignments

Asymmetric Unit
   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:245
 aligned with DFFB_MOUSE | O54788 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:245
                                    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324     
           DFFB_MOUSE    85 VSDITRFLSVFNEPHAGVIQAARQLLSDEQAPLRQKLLADLLHHVSQNITAETREQDPSWFEGLESRFRNKSGYLRYSCESRIRGYLREVSAYTSMVDEAAQEEYLRVLGSMCQKLKSVQYNGSYFDRGAEASSRLCTPEGWFSCQGPFDLESCLSKHSINPYGNRESRILFSTWNLDHIIEKKRTVVPTLAEAIQDGREVNWEYFYSLLFTAENLKLVHIACHKKTTHKLECDRSRIYRPQTGS 329
               SCOP domains d1v0da_ A: Caspase-activated DNase, CAD (DffB, DFF40)                                                                                                                                                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------DFF40-1v0dA01 A:101-324                                                                                                                                                                                                         ----- Pfam domains
         Sec.struct. author ..hhhhhhhhh......hhhhhhhhhhh..hhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...............ee..............eehhhhhhhhhhhh...eeee......hhhhhhhhhhhhh...hhhhhhhhhhh...eeeehhhhh..................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v0d A  85 VSDITRFLSVFNEPHAGVIQAARQQLSDEQAPLRQKLLADLLHHVSQNITAETREQDPSWFEGLESRFRNKSGYLRYSCESRIRGYLREVSAYTSMVDEAAQEEYLRVLGSMCQKLKSVQYNGSYFDRGAEASSRLCTPEGWFSCQGPFDLESCLSKHSINPYGNRESRILFSTWNLDHIIEKKRTVVPTLAEAIQDGREVNWEYFYSLLFTAENLKLVHIACHKKTTHKLECDRSRIYRPQTGS 329
                                    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324     

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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)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1V0D)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (15, 15)

Asymmetric Unit(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

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

UniProtKB/Swiss-Prot
        DFFB_MOUSE | O547881c9f 1f2r

(-) Related Entries Specified in the PDB File

1c9f NMR STRUCTURE OF THE CAD DOMAIN OF CASPASE -ACTIVATED DNASE
1f2r NMR STRUCTURE OF THE HETERODIMERIC COMPLEX BETWEEN CAD DOMAINS OF CAD AND ICAD