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(-) Description

Title :  CRYSTAL STRUCTURE OF TDP2 FROM DANIO RERIO COMPLEXED WITH A SINGLE STRAND DNA
 
Authors :  K. Shi, K. Kurahashi, H. Aihara
Date :  06 May 12  (Deposition) - 31 Oct 12  (Release) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.66
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  5'-Tyrosyl Dna Phosphodiesterase, 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 - DNA (5'-D(P*TP*GP*CP*AP*G)-3')
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - TYROSYL-DNA PHOSPHODIESTERASE 2
    Chains: A
    EC Number: 3.1.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    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 3 - TYROSYL-DNA PHOSPHODIESTERASE 2
    Chains: B
    EC Number: 3.1.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    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

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MG1Ligand/IonMAGNESIUM ION
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG C:5BINDING SITE FOR RESIDUE PO4 C 101
2AC2SOFTWAREGLN A:299 , HIS A:301 , CYS A:302 , HIS A:342 , MET A:343 , HOH A:517 , HOH A:670 , HOH A:762 , HOH A:763 , LEU B:178BINDING SITE FOR RESIDUE GOL A 401
3AC3SOFTWAREGLU A:161 , HOH A:531 , HOH A:678 , DT C:1BINDING SITE FOR RESIDUE MG A 402
4AC4SOFTWAREGLY A:186 , TYR A:187 , PHE A:200 , LEU A:201 , MET A:213 , MET A:214 , HOH A:505 , HOH A:560 , HOH A:598 , HOH A:772BINDING SITE FOR RESIDUE GOL A 403
5AC5SOFTWAREARG B:303 , ARG B:323 , ARG B:326 , HOH B:675 , HOH B:782BINDING SITE FOR RESIDUE GOL B 401
6AC6SOFTWARELEU B:138 , ALA B:165 , TYR B:166BINDING SITE FOR RESIDUE GOL B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F1H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4F1H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F1H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F1H)

(-) Exons   (0, 0)

(no "Exon" information available for 4F1H)

(-) 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....eeeeeeeee........eeeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeeeee...hhhhhhh.......eeehhhhh..hhhhh..ee.............ee..eeeeee........eeeeeeee...............eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f1h 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:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhh..eeeee......eeeeeee....eeeeeeeee........eeeeeeeee..eeeeeeee....hhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.......hhhhh.....eeehhhhh..hhhhh..ee.............ee..eeeeee.........eeeeeee...............eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f1h B 119 EDSKLSIISWNVDGLDTLNLADRARGLCSYLALYTPDVVFLQELIPAYVQYLKKRAVSYLFFEGSDDGYFTGIMLRKSRVKFLESEIICFPTTQMMRNLLIAQVTFSGQKLYLMTSHLESCKNQSQERTKQLRVVLQKIKEAPEDAIVIFAGDTNLRDAEVANVGGLPAGVCDVWEQLGKQEHCRYTWDTKANSNKTVPYVSRCRFDRIFLRSAKTAPPVTPDHMALIGMEKLDCGRYTSDHWGIYCTFNT 369
                                   128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368 


Chain C from PDB  Type:DNA  Length:5
                                     
                 4f1h C   1 TGCAG   5
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 4F1H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F1H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F1H)

(-) 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: 4fpv

(-) Related Entries Specified in the PDB File

4f1i 4fpv 4fva 4gew