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(-) Description

Title :  CRYSTAL STRUCTURE OF NURA WITH 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 :  3.15
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, 19)

Asymmetric/Biological Unit (3, 19)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MN4Ligand/IonMANGANESE (II) ION
3MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:51 , ASP A:126 , HOH A:455 , HOH A:466BINDING SITE FOR RESIDUE MN A 452
2AC2SOFTWAREASP A:51 , ASP A:126 , HIS A:411 , HOH A:455BINDING SITE FOR RESIDUE MN A 453
3AC3SOFTWAREGLU A:102 , GLU A:105 , ASN A:106 , ASP A:126 , GLY A:127 , HOH A:456 , HOH A:467BINDING SITE FOR RESIDUE GOL A 454
4AC4SOFTWAREASP B:51 , ASP B:126 , MN B:453 , HOH B:454 , HOH B:458BINDING SITE FOR RESIDUE MN B 452
5AC5SOFTWAREASP B:51 , ASP B:126 , HIS B:411 , MN B:452BINDING SITE FOR RESIDUE MN B 453

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TAL)

(-) 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:424
 aligned with NURA_PYRFU | Q8U1N8 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:434
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435    
           NURA_PYRFU     6 KQSIERITKILLDELENVRENEQIRNIINSWKPLPSPEKSSIYAVDGSRSVSRLSGTVIYFLSALAVGSGKQLRLSYANAIKSNYGTSDQIVRMQMETLENMLGYLAYRKLEGEKRAILMDGTLTGSLVRPPVYPEDIRSLNVMRALIGESDFENLLNEFLEKLRDHYRKVEEHLEKNGNYDSPILTDNVVEKLRKKYIDTKVIAYGSGKVKVKIPRKALGYSPRVIPIEVLESSRGKSVDELLQELDEEKVELYLGKDDIYDALHMTLSYIEYLYSIDKLLEVKNLAYIAKSFYTKTLARTLGVEIVDTALLDAVIRTLIGHEKEGYLEIEHAVVPPKWSFPDFLLSKFRNIEKLIDKGIHLAYVRFEQGDVIYMLQSTTNIEKILPLILHHKAGGYLRPLQLAHHGVKISYKEARHTLEALINALRNRDPAL 439
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh..hhhhhhhh..........eeeeeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee....hhhhhhhhhhhhhh...eeee...eeeee...-------.eeehhhhhhh...hhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhh.......hhhhhhhhhhhhh.....eeee............hhhhhh.hhhhhhhhhhh.eeeeee......eeeeee..hhhhhhhhhhh......hhhhhhhhhh..---.hhhhhhh.hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tal A   6 KQSIERITKILLDELENVRENEQIRNIINSWKPLPSPEKSSIYAVDGSRSVSRLSGTVIYFLSALAVGSGKQLRLSYANAIKSNYGTSDQIVRmQmETLENmLGYLAYRKLEGEKRAILmDGTLTGSLVRPPVYPEDIRSLNVmRALIGESDFENLLNEFLEKLRDHYRKVEEHLEKNGNYDSPILTDNVVEKLRKKYIDTKVIAYGSGKVKVKIPR-------RVIPIEVLESSRGKSVDELLQELDEEKVELYLGKDDIYDALHmTLSYIEYLYSIDKLLEVKNLAYIAKSFYTKTLARTLGVEIVDTALLDAVIRTLIGHEKEGYLEIEHAVVPPKWSFPDFLLSKFRNIEKLIDKGIHLAYVRFEQGDVIYmLQSTTNIEKILPLILHHKAGGYLRPLQLAHHGVK---KEARHTLEALINALRNRDPAL 439
                                    15        25        35        45        55        65        75        85        95   | | 105 |     115       125       135       145   |   155       165       175       185       195       205       215      |  -    |  235       245       255       265      |275       285       295       305       315       325       335       345       355       365       375     | 385       395       405       415   |   425       435    
                                                                                                                        99-MSE   |               125-MSE                 149-MSE                                                                  222     230                                       272-MSE                                                                                                      381-MSE                           415 419                    
                                                                                                                         101-MSE |                                                                                                                                                                                                                                                                                                                                            
                                                                                                                               107-MSE                                                                                                                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:421
 aligned with NURA_PYRFU | Q8U1N8 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:436
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434      
           NURA_PYRFU     5 SKQSIERITKILLDELENVRENEQIRNIINSWKPLPSPEKSSIYAVDGSRSVSRLSGTVIYFLSALAVGSGKQLRLSYANAIKSNYGTSDQIVRMQMETLENMLGYLAYRKLEGEKRAILMDGTLTGSLVRPPVYPEDIRSLNVMRALIGESDFENLLNEFLEKLRDHYRKVEEHLEKNGNYDSPILTDNVVEKLRKKYIDTKVIAYGSGKVKVKIPRKALGYSPRVIPIEVLESSRGKSVDELLQELDEEKVELYLGKDDIYDALHMTLSYIEYLYSIDKLLEVKNLAYIAKSFYTKTLARTLGVEIVDTALLDAVIRTLIGHEKEGYLEIEHAVVPPKWSFPDFLLSKFRNIEKLIDKGIHLAYVRFEQGDVIYMLQSTTNIEKILPLILHHKAGGYLRPLQLAHHGVKISYKEARHTLEALINALRNRDPALK 440
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh....hhhhh.ee........eeeeeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee....hhhhhhhhhhhhhh....------.ee.............eeehhhhhhhh..hhhhhhhhhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhh---....hhhhhhhhhhh..---..eeee............hhhhhh.hhhhhhhhhhh.eeeeee.......eeeee..hhhhhhhhhhh...---.hhhhhhhhhhh...hhhhhhhhhhhh....hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tal B   5 SKQSIERITKILLDELENVRENEQIRNIINSWKPLPSPEKSSIYAVDGSRSVSRLSGTVIYFLSALAVGSGKQLRLSYANAIKSNYGTSDQIVRmQmETLENmLGYLAYRKLEGEKRAILmDGTLTGSLVRPPVYPEDIRSLNVmRALIGESDFENLLNEFLEKLRDHYRKVEEHLEKNGNYDSPILTDNVVEKLRKKYIDTKV------KVKVKIPRKALGYSPRVIPIEVLESSRGKSVDELLQELDEEKVELYLGKDDIYDALHmTLSYIEYLYSIDKLLEVKNLAYIAKSFYTKTLAR---VEIVDTALLDAVIRTLI---KEGYLEIEHAVVPPKWSFPDFLLSKFRNIEKLIDKGIHLAYVRFEQGDVIYmLQSTTNIEKILPLILHHKA---LRPLQLAHHGVKISYKEARHTLEALINALRNRDPALK 440
                                    14        24        34        44        54        64        74        84        94    | |104  |    114       124|      134       144    |  154       164       174       184       194       204   |     -|      224       234       244       254       264       274       284       294       304 |   | 314       324 |   | 334       344       354       364       374      |384       394     | 404       414       424       434      
                                                                                                                         99-MSE   |               125-MSE                 149-MSE                                                    208    215                                                      272-MSE                           306 310             326 330                                                381-MSE            400 404                                    
                                                                                                                          101-MSE |                                                                                                                                                                                                                                                                                                                                             
                                                                                                                                107-MSE
   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 3TAL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 3taz

(-) Related Entries Specified in the PDB File

3tai SAME PROTEIN OF APO FORM
3taz