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(-) Description

Title :  CRYSTAL STRUCTURE OF TDP2 FROM C. ELEGANS
 
Authors :  K. Shi, K. Kurahashi, H. Aihara
Date :  02 Aug 12  (Deposition) - 31 Oct 12  (Release) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  5'-Phosphotyrosyl-Dna Diesterase, Hydrolase (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 - 5'-TYROSYL-DNA PHOSPHODIESTERASE
    Chains: A
    EC Number: 3.1.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-362
    Gene: Y63D3A.4
    Organism Common: NEMATODE
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
    Synonym: 5'-TYR-DNA PHOSPHODIESTERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1GOL9Ligand/IonGLYCEROL
Biological Unit 1 (1, 18)
No.NameCountTypeFull Name
1GOL18Ligand/IonGLYCEROL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:31 , GLU A:158 , HIS A:232 , SER A:235 , ASP A:271 , ASN A:273 , TRP A:303 , PHE A:321 , HIS A:353BINDING SITE FOR RESIDUE GOL A 401
2AC2SOFTWARELYS A:175 , ILE A:176 , HOH A:572BINDING SITE FOR RESIDUE GOL A 402
3AC3SOFTWAREGLY A:285 , TRP A:326 , GLY A:328 , LEU A:330 , ASP A:331BINDING SITE FOR RESIDUE GOL A 403
4AC4SOFTWAREASN A:150 , PRO A:151 , ASP A:152 , SER A:192BINDING SITE FOR RESIDUE GOL A 404
5AC5SOFTWAREALA A:141 , GLN A:341 , ILE A:343 , HOH A:541BINDING SITE FOR RESIDUE GOL A 405
6AC6SOFTWAREILE A:176 , TYR A:177 , TYR A:178 , HIS A:200 , HOH A:636BINDING SITE FOR RESIDUE GOL A 406
7AC7SOFTWAREALA A:292 , LYS A:332 , VAL A:333BINDING SITE FOR RESIDUE GOL A 407
8AC8SOFTWAREGLU A:113 , PRO A:329BINDING SITE FOR RESIDUE GOL A 408
9AC9SOFTWAREGLU A:113 , LEU A:115 , ARG A:342BINDING SITE FOR RESIDUE GOL A 409

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GEW)

(-) 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:324
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhh.......eeeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhh.eeeee.......eeeeeee..eeeeeeeeee........eeeeeeeee..eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhh.......eehhhhh..hhhhh..ee.............ee..eeeeee....eeeeeee................eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gew A  21 EDSEVEIEILDEPEQGKLSMSDEQKLHEFAIITATDEAFAQSILQDVDWDLKKALDVFYGSEAFAEARSAAVMGEDLKGFEVSVMSWNIDGLDGRSLLTRMKAVAHIVKNVNPDILFLQEVVDRDLAPIDKLQSLYKIYYSNKGCQYYTAILVSKMFDVEKHDVIHFQNSGMYRTLQILEGSIGGLKVFLLNTHLESTREHRPQRCAQFGFCMDKVREIIAQNPGALVFFGGDLNLRDEEVSRVPDGVKDAWEAAGSDNKTKFTWDTFKNDNKQGFHGAKMRFDRLYWSGPLDKVKFTLEGRQRIRSCLCFPSDHWAINATFFA 362
                                    30       |43        53        63        73        83        93   ||  118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358    
                                            38|                                                     97|                                                                                                                                                                                                                                                         
                                             42                                                     113
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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 4GEW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        TYDP2_CAEEL | Q9XWG3: 4f1i 4fva

(-) Related Entries Specified in the PDB File

4f1h 4f1i 4fpv 4fva