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(-) Description

Title :  MUS MUSCULUS TDP2 EXCLUDED SSDNA COMPLEX
 
Authors :  M. J. Schellenberg, R. S. Williams
Date :  05 Sep 12  (Deposition) - 31 Oct 12  (Release) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Protein-Dna Complex, Dna Repair, 5'-Dna End Processing, Endonuclease/Exonuclease/Phosphatase Domain, Eep Domain, 5'-Dna End Recognition, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Schellenberg, C. D. Appel, S. Adhikari, P. D. Robertson, D. A. Ramsden, R. S. Williams
Mechanism Of Repair Of 5'-Topoisomerase Ii-Dna Adducts By Mammalian Tyrosyl-Dna Phosphodiesterase 2.
Nat. Struct. Mol. Biol. V. 19 1363 2012
PubMed-ID: 23104055  |  Reference-DOI: 10.1038/NSMB.2418

(-) 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
    Fragment: UNP RESIDUES 118-369
    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(*CP*AP*TP*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
    Chains: D, C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 
Biological Unit 3 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:304 , ARG A:324BINDING SITE FOR RESIDUE FMT A 401
2AC2SOFTWAREASP A:132 , GLU A:162 , HOH A:556 , HOH A:557 , HOH A:603 , DT D:3BINDING SITE FOR RESIDUE MG A 402
3AC3SOFTWAREHOH A:612 , HOH A:613 , HOH C:231 , HOH D:210 , HOH D:219 , HOH D:220BINDING SITE FOR RESIDUE MG D 101
4AC4SOFTWAREASP B:156 , ARG B:198 , HOH B:651BINDING SITE FOR RESIDUE FMT B 401
5AC5SOFTWAREASP B:132 , GLU B:162 , HOH B:577 , HOH B:587 , HOH B:628 , DT C:3BINDING SITE FOR RESIDUE MG B 402
6AC6SOFTWAREHOH C:207 , HOH C:208 , HOH C:211 , HOH C:218 , HOH C:230 , HOH D:218BINDING SITE FOR RESIDUE MG C 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GZ2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GZ2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GZ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GZ2)

(-) Exons   (0, 0)

(no "Exon" information available for 4GZ2)

(-) Sequences/Alignments

Asymmetric 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:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhh..eeee.......eeeeeee...eeeeeeeeee........eeeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhhh......eeeeeee.....hhhhhh......eeehhhhh..hhhhh..ee.............ee..eeeeee.....eeeeeeeee...............eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gz2 A 122 STISFITWNIDGLDGCNLPERARGVCSCLALYSPDVVFLQEVIPPYCAYLKKRAASYTIITGNEEGYFTAILLKKGRVKFKSQEIIPFPNTKMMRNLLCVNVSLGGNEFCLMTSHLESTREHSAERIRQLKTVLGKMQEAPDSTTVIFAGDTNLRDQEVIKCGGLPDNVFDAWEFLGKPKHCQYTWDTKANNNLRIPAAYKHRFDRIFFRAEEGHLIPQSLDLVGLEKLDCGRFPSDHWGLLCTLNVV 369
                                   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 B from PDB  Type:PROTEIN  Length:246
                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhh..eeeee......eeeeeee....eeeeeeeee........eeeeeeeee..eeeeeeee....hhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....hhhhhh......eeehhhhh..hhhhh..ee.............ee..eeeeee...eeeeeeeee...............eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gz2 B 122 STISFITWNIDGLDGCNLPERARGVCSCLALYSPDVVFLQEVIPPYCAYLKKRAASYTIITGNEEGYFTAILLKKGRVKFKSQEIIPFPNTKMMRNLLCVNVSLGGNEFCLMTSHLESTREHSAERIRQLKTVLGKMQEAPDSTTVIFAGDTNLRDQEVIKCGGLPDNVFDAWEFLGKPKHCQYTWDTKANNNLRIPAAYKHRFDRIFFRAGHLIPQSLDLVGLEKLDCGRFPSDHWGLLCTLNVV 369
                                   131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331||     343       353       363      
                                                                                                                                                                                                                                            332|                                  
                                                                                                                                                                                                                                             335                                  


Chain C from PDB  Type:DNA  Length:12
                                            
                 4gz2 C   1 CATCCGAATTCG  12
                                    10  


Chain D from PDB  Type:DNA  Length:12
                                            
                 4gz2 D   1 CATCCGAATTCG  12
                                    10
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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 4GZ2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GZ2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GZ2)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)

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  4gz2
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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 4puq 5ht2 5ink 5inl 5inm 5inn 5inp 5inq 5j3z 5j42

(-) Related Entries Specified in the PDB File

4gyz 4gz0 4gz1