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(-) Description

Title :  MUS MUSCULUS TDP2 REACTION PRODUCT (5'-PHOSPHORYLATED DNA)-MG2+ COMPLEX AT 1.5 ANGSTROMS RESOLUTION
 
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 :  1.50
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 118-370
    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*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
    Chains: C, D
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED DNA
    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  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2FMT1Ligand/IonFORMIC ACID
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2FMT-1Ligand/IonFORMIC ACID
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2FMT1Ligand/IonFORMIC ACID
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2FMT1Ligand/IonFORMIC ACID
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:210 , HOH A:567 , HOH A:633 , ILE B:180 , ILE B:181 , PHE B:201 , HOH B:507BINDING SITE FOR RESIDUE EPE A 401
2AC2SOFTWAREGLU A:162 , HOH A:616 , HOH A:735 , HOH A:739 , DC D:1 , HOH D:104BINDING SITE FOR RESIDUE MG A 402
3AC3SOFTWARECYS B:149 , TYR B:153 , VAL B:345 , GLY B:346 , LEU B:347BINDING SITE FOR RESIDUE FMT B 401
4AC4SOFTWAREGLU B:162 , HOH B:596 , HOH B:597 , HOH B:598 , DC C:1 , HOH C:118BINDING SITE FOR RESIDUE MG B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GZ1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GZ1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GZ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GZ1)

(-) Exons   (0, 0)

(no "Exon" information available for 4GZ1)

(-) 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:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhh.eeeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhh..eeeee......eeeeeee...eeeeeeeeee........eeeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhh.....eeehhhhh..hhhhh..ee.............ee..eeeeee....eeeeeeeee...............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gz1 A 116 NGLEDSSTISFITWNIDGLDGCNLPERARGVCSCLALYSPDVVFLQEVIPPYCAYLKKRAASYTIITGNEEGYFTAILLKKGRVKFKSQEIIPFPNTKMMRNLLCVNVSLGGNEFCLMTSHLESTREHSAERIRQLKTVLGKMQEAPDSTTVIFAGDTNLRDQEVIKCGGLPDNVFDAWEFLGKPKHCQYTWDTKANNNLRIPAAYKHRFDRIFFRAEGHLIPQSLDLVGLEKLDCGRFPSDHWGLLCTLNVVL 370
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325      |336       346       356       366    
                                                                                                                                                                                                                                                  332|                                    
                                                                                                                                                                                                                                                   334                                    


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..eeeeeee.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhh......eehhhhh..hhhhh..ee.............ee..eeeeee......eeeeeeee...............eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gz1 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
                                         
                 4gz1 C   1 CCGAATTCG   9


Chain D from PDB  Type:DNA  Length:9
                                         
                 4gz1 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 4GZ1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GZ1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GZ1)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)

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  4gz1
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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 4gz2 4puq 5ht2 5ink 5inl 5inm 5inn 5inp 5inq 5j3z 5j42

(-) Related Entries Specified in the PDB File

4gyz 4gz0 4gz2