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(-) Description

Title :  MUS MUSCULUS TDP2 REACTION PRODUCT COMPLEX WITH 5'-PHOSPHORYLATED RNA/DNA, GLYCEROL, AND MG2+
 
Authors :  M. J. Schellenberg, R. S. Williams
Date :  13 Mar 14  (Deposition) - 14 May 14  (Release) - 23 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein-Dna Complex, Dna Repair, 5'-Dna End Processing, Eep Domain, Hydrolase, Metalloenzyme, 5'-Dna End Recognition, Hydrolase-Dna-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Gao, M. J. Schellenberg, S. Y. Huang, M. Abdelmalak, C. Marchand, K. C. Nitiss, J. L. Nitiss, R. S. Williams, Y. Pommier
Proteolytic Degradation Of Topoisomerase Ii (Top2) Enables The Processing Of Top2Dna And Top2Rna Covalent Complexes By Tyrosyl-Dna-Phosphodiesterase 2 (Tdp2).
J. Biol. Chem. V. 289 17960 2014
PubMed-ID: 24808172  |  Reference-DOI: 10.1074/JBC.M114.565374

(-) 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
    Expression System Vector Type: PLASMID
    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/RNA HYBRID
    Chains: C, D
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED NUCLEIC ACID
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL3Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:162 , HOH A:612 , HOH A:701 , HOH A:704 , C D:1 , HOH D:202BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREGLU B:162 , GOL B:402 , HOH B:592 , HOH B:593 , HOH B:594 , C C:1BINDING SITE FOR RESIDUE MG B 401
3AC3SOFTWARELEU B:134 , GLU B:162 , ARG B:216 , SER B:239 , MG B:401 , HOH B:593 , HOH B:650 , HOH B:703 , HOH B:710 , C C:1BINDING SITE FOR RESIDUE GOL B 402
4AC4SOFTWAREASP A:288 , PRO B:300 , HIS B:302 , GLN B:340 , SER B:341 , LEU B:342 , HOH B:588 , HOH B:677 , HOH B:686 , HOH B:759BINDING SITE FOR RESIDUE GOL B 403
5AC5SOFTWARELEU A:315 , HOH C:104 , C D:1 , DC D:2 , HOH D:209BINDING SITE FOR RESIDUE ACT D 101
6AC6SOFTWAREGLU A:242 , HOH C:112 , HOH C:119 , C D:1 , DC D:2 , DG D:3 , HOH D:221BINDING SITE FOR RESIDUE GOL D 102

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PUQ)

(-) 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:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.eeeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhh..eeeee......eeeeeee...eeeeeeeeee........eeeeeeeee..eeeeeeee....hhhhhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhh.......eeehhhhh..hhhhh..ee.............ee..eeeeee.....eeeeeeeee...............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4puq A 115 SNGLEDSSTISFITWNIDGLDGCNLPERARGVCSCLALYSPDVVFLQEVIPPYCAYLKKRAASYTIITGNEEGYFTAILLKKGRVKFKSQEIIPFPNTKMMRNLLCVNVSLGGNEFCLMTSHLESTREHSAERIRQLKTVLGKMQEAPDSTTVIFAGDTNLRDQEVIKCGGLPDNVFDAWEFLGKPKHCQYTWDTKANNNLRIPAAYKHRFDRIFFRAEEGHLIPQSLDLVGLEKLDCGRFPSDHWGLLCTLNVVL 370
                                   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      


Chain B from PDB  Type:PROTEIN  Length:249
                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhh..eeeee......eeeeeee....eeeeeeeee........eeeeeeeee..eeeeeeee....hhhhhhhhhhhhhhhhhhhh......eeeeeee...hhhhhhhhh......eehhhhh..hhhhh..ee.............ee..eeeeee......eeeeeeee...............eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4puq B 122 STISFITWNIDGLDGCNLPERARGVCSCLALYSPDVVFLQEVIPPYCAYLKKRAASYTIITGNEEGYFTAILLKKGRVKFKSQEIIPFPNTKMMRNLLCVNVSLGGNEFCLMTSHLESTREHSAERIRQLKTVLGKMQEAPDSTTVIFAGDTNLRDQEVIKCGGLPDNVFDAWEFLGKPKHCQYTWDTKANNNLRIPAAYKHRFDRIFFRAEEGHLIPQSLDLVGLEKLDCGRFPSDHWGLLCTLNVVL 370
                                   131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361         


Chain C from PDB  Type:DNA/RNA  Length:9
                                         
                 4puq C   1 CCGAATTCG   9


Chain D from PDB  Type:DNA/RNA  Length:9
                                         
                 4puq D   1 CCGAATTCG   9
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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 4PUQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)

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  4puq
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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 5ht2 5ink 5inl 5inm 5inn 5inp 5inq 5j3z 5j42

(-) Related Entries Specified in the PDB File

4gz1