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(-) Description

Title :  MOUSE TDP2 REACTION PRODUCT (5'-PHOSPHORYLATED DNA)-ABASIC/THF-MG2+ COMPLEX
 
Authors :  M. J. Schellenberg, R. S. Williams
Date :  07 Mar 16  (Deposition) - 27 Apr 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hydrolase, Dna Repair, Endonuclease/Exonuclease/Phosphatase (Eep) Domain, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Schellenberg, L. Perera, C. N. Strom, C. A. Waters, B. Monian, C. D. Appel, C. K. Vilas, J. G. Williams, D. A. Ramsden, R. S. Williams
Reversal Of Dna Damage Induced Topoisomerase 2 Dna-Protein Crosslinks By Tdp2.
Nucleic Acids Res. V. 44 3829 2016
PubMed-ID: 27060144  |  Reference-DOI: 10.1093/NAR/GKW228

(-) Compounds

Molecule 1 - TYROSYL-DNA PHOSPHODIESTERASE 2
    Chains: A, B
    EC Number: 3.1.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG9
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 118-370
    Gene: TDP2, TTRAP
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: TYR-DNA PHOSPHODIESTERASE 2,5'-TYROSYL-DNA PHOSPHODIESTERASE,5'-TYR-DNA PHOSPHODIESTERASE,TRAF AND TNF RECEPTOR- ASSOCIATED PROTEIN
 
Molecule 2 - DNA (5'-D(P*(3DR)P*CP*GP*AP*AP*TP*TP*CP*G)-3')
    Chains: C, D
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric/Biological Unit (5, 7)
No.NameCountTypeFull Name
13DR2Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3GOL1Ligand/IonGLYCEROL
4MG2Ligand/IonMAGNESIUM ION
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:209 , PRO A:210 , ASN A:211 , GLU A:246 , ARG A:249 , THR A:253binding site for residue GOL A 401
2AC2SOFTWAREGLU A:162 , HOH A:519 , HOH A:534 , HOH A:538 , 3DR D:1 , HOH D:109binding site for residue MG A 402
3AC3SOFTWAREGLU B:162 , HOH B:523 , HOH B:528 , HOH B:531 , 3DR C:1 , HOH C:107binding site for residue MG B 401
4AC4SOFTWARECYS B:149 , TYR B:153 , VAL B:345 , GLY B:346 , LEU B:347binding site for residue EPE B 402
5AC5SOFTWAREPRO A:208 , ILE B:180 , ILE B:181binding site for residue PEG B 403
6AC6SOFTWAREASN B:130 , GLU B:162 , HIS B:236 , SER B:239 , THR B:240 , ASP B:272 , ASN B:274 , ARG B:276 , TRP B:307 , ILE B:317 , TYR B:321 , PHE B:325 , HIS B:359 , MG B:401 , HOH B:528 , HOH B:531 , DG C:3 , HOH C:101 , HOH C:102 , HOH C:103 , HOH C:105 , HOH C:107 , HOH C:109 , DC D:8 , DG D:9binding site for Di-nucleotide 3DR C 1 and DC C 2
7AC7SOFTWAREASN A:130 , GLU A:162 , HIS A:236 , SER A:239 , THR A:240 , ASP A:272 , ASN A:274 , ARG A:276 , TRP A:307 , ILE A:317 , TYR A:321 , HIS A:323 , HIS A:359 , MG A:402 , HOH A:519 , HOH A:534 , DC C:8 , DG C:9 , DG D:3 , HOH D:101 , HOH D:102 , HOH D:107 , HOH D:109binding site for Di-nucleotide 3DR D 1 and DC D 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5INK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5INK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5INK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5INK)

(-) Exons   (0, 0)

(no "Exon" information available for 5INK)

(-) 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:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh.eeeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhh..eeeee......eeeeeee....eeeeeeeee........eeeeeeeee..eeeeeeee....hhhhhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhh.....eeehhhhh..hhhhh..ee.............ee..eeeeee.....eeeeeeeee...............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ink A 117 GLEDSSTISFITWNIDGLDGCNLPERARGVCSCLALYSPDVVFLQEVIPPYCAYLKKRAASYTIITGNEEGYFTAILLKKGRVKFKSQEIIPFPNTKMMRNLLCVNVSLGGNEFCLMTSHLESTREHSAERIRQLKTVLGKMQEAPDSTTVIFAGDTNLRDQEVIKCGGLPDNVFDAWEFLGKPKHCQYTWDTKANNNLRIPAAYKHRFDRIFFRAEEGHLIPQSLDLVGLEKLDCGRFPSDHWGLLCTLNVVL 370
                                   126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366    


Chain B from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhh..eeeee......eeeeeee....eeeeeeeee........eeeeeeeee..eeeeeeee....hhhhhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhh.......eehhhhh.........ee.............ee..eeeeee.....eeeeeeeee...............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ink B 123 TISFITWNIDGLDGCNLPERARGVCSCLALYSPDVVFLQEVIPPYCAYLKKRAASYTIITGNEEGYFTAILLKKGRVKFKSQEIIPFPNTKMMRNLLCVNVSLGGNEFCLMTSHLESTREHSAERIRQLKTVLGKMQEAPDSTTVIFAGDTNLRDQEVIKCGGLPDNVFDAWEFLGKPKHCQYTWDTKANNNLRIPAAYKHRFDRIFFRAEEGHLIPQSLDLVGLEKLDCGRFPSDHWGLLCTLNVVL 370
                                   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:9
                                         
                 5ink C   1 xCGAATTCG   9
                            |        
                            1-3DR    


Chain D from PDB  Type:DNA  Length:9
                                         
                 5ink D   1 xCGAATTCG   9
                            |        
                            1-3DR
   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 5INK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5INK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5INK)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)

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  5ink
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  TYDP2_MOUSE | Q9JJX7
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  3.1.4.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        TYDP2_MOUSE | Q9JJX7: 4gyz 4gz0 4gz1 4gz2 4puq 5ht2 5inl 5inm 5inn 5inp 5inq 5j3z 5j42

(-) Related Entries Specified in the PDB File

4gz1 4GZ1 CONTAINS THE SAME MOLECULE COMPLEXED WITH A DIFFERENT DNA
5inl
5inm
5inn
5inp
5inq