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(-) Description

Title :  CRYSTAL STRUCTURE OF CED-3 PROTEASE SUPPRESSOR-6 (CPS-6) FROM CAENORHABDITIS ELEGANS
 
Authors :  H. S. Yuan, J. L. J. Lin
Date :  23 May 11  (Deposition) - 11 Jan 12  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna Fragmentation, Nuclease, Dnase, Protein-Dna Interactions, Beta- Beta-Alpha-Metal Finger Nuclease, Hydrolase, Mitochondria (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. L. J. Lin, A. Nakagawa, C. L. Lin, Y. Y. Hsiao, W. Z. Yang, Y. T. Wang, L. G. Doudeva, R. R. Skeen-Gaar, D. Xue, H. S. Yuan
Structural Insights Into Apoptotic Dna Degradation By Ced-3 Protease Suppressor-6 (Cps-6) From Caenorhabditis Elegans
J. Biol. Chem. V. 287 7110 2012
PubMed-ID: 22223640  |  Reference-DOI: 10.1074/JBC.M111.316075

(-) Compounds

Molecule 1 - ENDONUCLEASE G
    ChainsA, B
    EC Number3.1.30.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE30
    Expression System StrainM15
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 63-303
    GeneCPS-6
    Organism ScientificCAENORHABDITIS ELEGANS
    Organism Taxid6239
    StrainBRISTOL N2
    SynonymCPS-6, ENDO G, CED-3 PROTEASE SUPPRESSOR 6

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:38 , ASN A:180 , HOH A:310 , HOH A:321 , HOH A:335BINDING SITE FOR RESIDUE MG A 1
2AC2SOFTWAREHOH B:15 , HOH B:29 , ASN B:180 , HOH B:334 , HOH B:402 , HOH B:412BINDING SITE FOR RESIDUE MG B 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3S5B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3S5B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S5B)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUCLEASE_NON_SPECPS01070 DNA/RNA non-specific endonucleases active site.NUCG_CAEEL145-153
 
  2A:145-153
B:145-153

(-) Exons   (0, 0)

(no "Exon" information available for 3S5B)

(-) Sequences/Alignments

Asymmetric/Biological 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:236
 aligned with NUCG_CAEEL | Q95NM6 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:241
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302 
           NUCG_CAEEL    63 PSRSAEIMKHGYPGFTNVRTYEDFVLSYDYKTRTAHWVCEHLTPERLKHAEGVDRKLCEFKPDITFPQKFLSQNTDYKCSGFDRGHLAAAGNHRKSQLAVDQTFYLSNMSPQVGRGFNRDKWNDLEMHCRRVAKKMINSYIITGPLYLPKLEGDGKKYIKYQVIGDNNVAVPTHFFKVALFEVTPGKFELESYILPNAVIEDTVEISKFHVPLDAVERSAGLEIFARLDPKSIVKENGAKK 303
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh.........eee....eeeee....eeeeeeeee.....-----.hhhhh........hhhhh.hhhhhh....eeee..hhhhh..hhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhh....eeeeeeee..eee.....eeeeeeee....ee...eeeeeeeeeee..eeeeeeeeee........hhhhhh.hhhhhhhhhh.......hhh.eeee..ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------NUCLEASE_------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s5b A  63 PSRSAEIMKHGYPGFTNVRTYEDFVLSYDYKTRTAHWVCEHLTPERL-----VDRKLCEFKPDITFPQKFLSQNTDYKCSGFDRGHLAAAGNHRKSQLAVDQTFYLSNMSPQVGRGFNRDKWNDLEMHCRRVAKKMINSYIITGPLYLPKLEGDGKKYIKYQVIGDNNVAVPTHFFKVALFEVTPGKFELESYILPNAVIEDTVEISKFHVPLDAVERSAGLEIFARLDPKSIVKENGAKK 303
                                    72        82        92       102      |  -  |    122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302 
                                                                        109   115                                                                                                                                                                                            

Chain B from PDB  Type:PROTEIN  Length:243
 aligned with NUCG_CAEEL | Q95NM6 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:243
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299   
           NUCG_CAEEL    60 AMGPSRSAEIMKHGYPGFTNVRTYEDFVLSYDYKTRTAHWVCEHLTPERLKHAEGVDRKLCEFKPDITFPQKFLSQNTDYKCSGFDRGHLAAAGNHRKSQLAVDQTFYLSNMSPQVGRGFNRDKWNDLEMHCRRVAKKMINSYIITGPLYLPKLEGDGKKYIKYQVIGDNNVAVPTHFFKVALFEVTPGKFELESYILPNAVIEDTVEISKFHVPLDAVERSAGLEIFARLDPKSIVKENGAK 302
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh.........eee....eeeee....eeeeeeeee.hhhhh.....hhhhh........hhhhh.hhhhhh....eeee..hhhhh..hhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhh...eeeeeeeee...ee.....eeeeeeee....ee...eeeeeeeeeee..eeeeeeeeee........hhhhhh.hhhhhhhhhh.......hhh.eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------NUCLEASE_----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s5b B  60 HGSPSRSAEIMKHGYPGFTNVRTYEDFVLSYDYKTRTAHWVCEHLTPERLKHAEGVDRKLCEFKPDITFPQKFLSQNTDYKCSGFDRGHLAAAGNHRKSQLAVDQTFYLSNMSPQVGRGFNRDKWNDLEMHCRRVAKKMINSYIITGPLYLPKLEGDGKKYIKYQVIGDNNVAVPTHFFKVALFEVTPGKFELESYILPNAVIEDTVEISKFHVPLDAVERSAGLEIFARLDPKSIVKENGAK 302
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299   

   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

(no "SCOP Domain" information available for 3S5B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S5B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3S5B)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NUCG_CAEEL | Q95NM6)
molecular function
    GO:0004520    endodeoxyribonuclease activity    Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    GO:0000737    DNA catabolic process, endonucleolytic    The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides.
    GO:0006401    RNA catabolic process    The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    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: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:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NUCG_CAEEL | Q95NM64qn0 5gkc 5gkp

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