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(-) Description

Title :  CRYSTAL STRUCTURE OF D. RERIO TDP2 COMPLEXED WITH SINGLE STRAND DNA PRODUCT
 
Authors :  K. Shi, K. Kurahashi, H. Aihara
Date :  22 Jun 12  (Deposition) - 31 Oct 12  (Release) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  5'-Phosphotyrosyl-Dna Diesterase, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Shi, K. Kurahashi, R. Gao, S. E. Tsutakawa, J. A. Tainer, Y. Pommier, H. Aihara
Structural Basis For Recognition Of 5'-Phosphotyrosine Adducts By Tdp2.
Nat. Struct. Mol. Biol. V. 19 1372 2012
PubMed-ID: 23104058  |  Reference-DOI: 10.1038/NSMB.2423

(-) Compounds

Molecule 1 - TYROSYL-DNA PHOSPHODIESTERASE 2
    Chains: A, B
    EC Number: 3.1.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 113-369
    Organism Common: LEOPARD DANIO,ZEBRA DANIO,ZEBRA FISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955
    Synonym: TYR-DNA PHOSPHODIESTERASE 2, 5'-TYROSYL-DNA PHOSPHODIESTERASE, 5'-TYR-DNA PHOSPHODIESTERASE, TRAF AND TNF RECEPTOR-ASSOCIATED PROTEIN HOMOLOG
 
Molecule 2 - DNA (5'-D(P*TP*GP*CP*AP*G)-3')
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MG2Ligand/IonMAGNESIUM ION
3NA2Ligand/IonSODIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:122 , ASP A:341 , THR A:366 , HOH A:722BINDING SITE FOR RESIDUE NA A 401
2AC2SOFTWAREASP A:276 , ALA A:277 , ARG A:323 , ARG A:326 , HOH A:542 , HOH A:672 , HOH A:673BINDING SITE FOR RESIDUE GOL A 402
3AC3SOFTWAREGLU B:161 , HOH B:527 , HOH B:632 , HOH B:648 , HOH B:649 , HOH B:727BINDING SITE FOR RESIDUE MG B 401
4AC4SOFTWAREASP B:341 , ASN B:368 , HOH B:713 , HOH B:741BINDING SITE FOR RESIDUE NA B 402
5AC5SOFTWAREARG B:275 , ASP B:276 , ARG B:303 , ARG B:323 , ARG B:326 , HOH B:661 , HOH B:689BINDING SITE FOR RESIDUE GOL B 403
6AC6SOFTWAREGLU B:181 , SER B:203 , GLU B:204 , HOH B:566 , HOH B:567BINDING SITE FOR RESIDUE GOL B 404
7AC7SOFTWAREGLU A:161 , HOH A:716 , HOH A:717 , HOH A:718 , DT C:1BINDING SITE FOR RESIDUE MG C 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FPV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4FPV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FPV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FPV)

(-) Exons   (0, 0)

(no "Exon" information available for 4FPV)

(-) 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:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhh..eeeee......eeeeeee...eeeeeeeeee........eeeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.......hhhhh.....eeehhhhh..hhhhh..ee.............ee..eeeeee........eeeeeeee...............eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fpv A 120 DSKLSIISWNVDGLDTLNLADRARGLCSYLALYTPDVVFLQELIPAYVQYLKKRAVSYLFFEGSDDGYFTGIMLRKSRVKFLESEIICFPTTQMMRNLLIAQVTFSGQKLYLMTSHLESCKNQSQERTKQLRVVLQKIKEAPEDAIVIFAGDTNLRDAEVANVGGLPAGVCDVWEQLGKQEHCRYTWDTKANSNKTVPYVSRCRFDRIFLRSAKTAPPVTPDHMALIGMEKLDCGRYTSDHWGIYCTFNT 369
                                   129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369


Chain B from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.eeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhh..eeeee......eeeeeee....eeeeeeeee........eeeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.......hhhhh.....eeehhhhh..hhhhh..ee.............ee..eeeeee.........eeeeeee...............eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fpv B 113 TAKSEVEDSKLSIISWNVDGLDTLNLADRARGLCSYLALYTPDVVFLQELIPAYVQYLKKRAVSYLFFEGSDDGYFTGIMLRKSRVKFLESEIICFPTTQMMRNLLIAQVTFSGQKLYLMTSHLESCKNQSQERTKQLRVVLQKIKEAPEDAIVIFAGDTNLRDAEVANVGGLPAGVCDVWEQLGKQEHCRYTWDTKANSNKTVPYVSRCRFDRIFLRSAKTAPPVTPDHMALIGMEKLDCGRYTSDHWGIYCTFNT 369
                                   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       


Chain C from PDB  Type:DNA  Length:5
                                     
                 4fpv C   1 TGCAG   5
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4FPV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FPV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FPV)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        TYDP2_DANRE | Q5XJA0: 4f1h

(-) Related Entries Specified in the PDB File

4f1h 4f1i 4fva 4gew