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(-) Description

Title :  CRYSTAL STRUCTURE OF NURA BOUND TO DAMP AND MANGANESE
 
Authors :  J. Chae, Y. C. Kim, Y. Cho
Date :  04 Aug 11  (Deposition) - 23 Nov 11  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Recombination, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Chae, Y. C. Kim, Y. Cho
Crystal Structure Of The Nura-Damp-Mn2+ Complex
Nucleic Acids Res. V. 40 2258 2012
PubMed-ID: 22064858  |  Reference-DOI: 10.1093/NAR/GKR999

(-) Compounds

Molecule 1 - DNA DOUBLE-STRAND BREAK REPAIR PROTEIN NURA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PF1168
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 186497
    Strain: ATCC 43587 / DSM 3638 / JCM 8422 / VC1
    Synonym: PUTATIVE UNCHARACTERIZED PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1DA1Ligand/Ion2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3MN2Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:51 , GLY A:52 , GLU A:105 , ASP A:126BINDING SITE FOR RESIDUE MN A 452
2AC2SOFTWARESER A:74 , SER A:239 , HIS A:397 , HIS A:398BINDING SITE FOR RESIDUE GOL A 453
3AC3SOFTWAREASP B:51 , ASP B:126BINDING SITE FOR RESIDUE MN B 452
4AC4SOFTWAREARG B:98 , GLU B:102 , GLY B:127 , THR B:128 , GLY B:131 , SER B:132 , ARG B:135 , PRO B:137 , PHE B:299 , HOH B:454BINDING SITE FOR RESIDUE DA B 453

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:139 -Pro A:140
2Gly B:226 -Tyr B:227
3Ser B:228 -Pro B:229
4Pro B:229 -Arg B:230

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TAZ)

(-) Exons   (0, 0)

(no "Exon" information available for 3TAZ)

(-) 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:432
 aligned with NURA_PYRFU | Q8U1N8 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:439
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432         
           NURA_PYRFU     3 LLSKQSIERITKILLDELENVRENEQIRNIINSWKPLPSPEKSSIYAVDGSRSVSRLSGTVIYFLSALAVGSGKQLRLSYANAIKSNYGTSDQIVRMQMETLENMLGYLAYRKLEGEKRAILMDGTLTGSLVRPPVYPEDIRSLNVMRALIGESDFENLLNEFLEKLRDHYRKVEEHLEKNGNYDSPILTDNVVEKLRKKYIDTKVIAYGSGKVKVKIPRKALGYSPRVIPIEVLESSRGKSVDELLQELDEEKVELYLGKDDIYDALHMTLSYIEYLYSIDKLLEVKNLAYIAKSFYTKTLARTLGVEIVDTALLDAVIRTLIGHEKEGYLEIEHAVVPPKWSFPDFLLSKFRNIEKLIDKGIHLAYVRFEQGDVIYMLQSTTNIEKILPLILHHKAGGYLRPLQLAHHGVKISYKEARHTLEALINALRNRDPALKI 441
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh.......hhhhh.........eeeeeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee....hhhhhhhhhhhhhh...eeee...eeeee....----....eehhhhhhh...hhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.....hhhhhh.---..hhhhhhhhhhh.......eeee.......hhhhhhhhhhh.hhhhhhhhhhh.eeeeee.......eeeee..hhhhhhhhhhh......hhhhhhhhhhhh........hhhhhhhhhh..hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3taz A   3 LLSKQSIERITKILLDELENVRENEQIRNIINSWKPLPSPEKSSIYAVDGSRSVSRLSGTVIYFLSALAVGSGKQLRLSYANAIKSNYGTSDQIVRMQMETLENMLGYLAYRKLEGEKRAILMDGTLTGSLVRPPVYPEDIRSLNVMRALIGESDFENLLNEFLEKLRDHYRKVEEHLEKNGNYDSPILTDNVVEKLRKKYIDTKVIAYGSGKVKVKIPRK----SPRVIPIEVLESSRGKSVDELLQELDEEKVELYLGKDDIYDALHMTLSYIEYLYSIDKLLEVKNLAYIAKSFYTKTLARTL---IVDTALLDAVIRTLIGHEKEGYLEIEHAVVPPKWSFPDFLLSKFRNIEKLIDKGIHLAYVRFEQGDVIYMLQSTTNIEKILPLILHHKAGGYLRPLQLAHHGVKISYKEARHTLEALINALRNRDPALKI 441
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222|    | 232       242       252       262       272       282       292       302     | 312       322       332       342       352       362       372       382       392       402       412       422       432         
                                                                                                                                                                                                                                                      223  228                                                                             308 312                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:433
 aligned with NURA_PYRFU | Q8U1N8 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:439
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432         
           NURA_PYRFU     3 LLSKQSIERITKILLDELENVRENEQIRNIINSWKPLPSPEKSSIYAVDGSRSVSRLSGTVIYFLSALAVGSGKQLRLSYANAIKSNYGTSDQIVRMQMETLENMLGYLAYRKLEGEKRAILMDGTLTGSLVRPPVYPEDIRSLNVMRALIGESDFENLLNEFLEKLRDHYRKVEEHLEKNGNYDSPILTDNVVEKLRKKYIDTKVIAYGSGKVKVKIPRKALGYSPRVIPIEVLESSRGKSVDELLQELDEEKVELYLGKDDIYDALHMTLSYIEYLYSIDKLLEVKNLAYIAKSFYTKTLARTLGVEIVDTALLDAVIRTLIGHEKEGYLEIEHAVVPPKWSFPDFLLSKFRNIEKLIDKGIHLAYVRFEQGDVIYMLQSTTNIEKILPLILHHKAGGYLRPLQLAHHGVKISYKEARHTLEALINALRNRDPALKI 441
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee....hhhhhhhhhhhhhhhhhh..----..eeeee.hhh.....ee.hhhhhhh...hhhhhhhhhhhheeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...........--....hhhhhhhhhhhhh.....eeee............hhhhhh.hhhhhhhhhhh.eeeeee......eeeeee..hhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3taz B   3 LLSKQSIERITKILLDELENVRENEQIRNIINSWKPLPSPEKSSIYAVDGSRSVSRLSGTVIYFLSALAVGSGKQLRLSYANAIKSNYGTSDQIVRMQMETLENMLGYLAYRKLEGEKRAILMDGTLTGSLVRPPVYPEDIRSLNVMRALIGESDFENLLNEFLEKLRDHYRKVEEHLEKNGNYDSPILTDNVVEKLRKKYIDTKVIA----KVKVKIPRKALGYSPRVIPIEVLESSRGKSVDELLQELDEEKVELYLGKDDIYDALHMTLSYIEYLYSIDKLLEVKNLAYIAKSFYTKTLART--VEIVDTALLDAVIRTLIGHEKEGYLEIEHAVVPPKWSFPDFLLSKFRNIEKLIDKGIHLAYVRFEQGDVIYMLQSTTNIEKILPLILHHKAGGYLRPLQLAHHGVKISYKEARHTLEALINALRNRDPALKI 441
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       | -  |    222       232       242       252       262       272       282       292       302    |  312       322       332       342       352       362       372       382       392       402       412       422       432         
                                                                                                                                                                                                                                         210  215                                                                                         307  |                                                                                                                                   
                                                                                                                                                                                                                                                                                                                                             310
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 3TAZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NURA_PYRFU | Q8U1N8)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    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.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage 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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NURA_PYRFU | Q8U1N8: 3tai 3tal

(-) Related Entries Specified in the PDB File

3tai SAME PROTEIN OF APO FORM
3tal SAME PROTEIN OF MN-BOUND FORM