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(-) Description

Title :  CRYSTAL STRUCTURE OF TRUNCATED CAENORHABDITIS ELEGANS TDP2
 
Authors :  K. Shi, K. Kurahashi, H. Aihara
Date :  29 Jun 12  (Deposition) - 31 Oct 12  (Release) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
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, B, C, D
    EC Number: 3.1.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 107-362
    Gene: Y63D3A.4
    Organism Common: NEMATODE
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
    Synonym: 5'-TYR-DNA PHOSPHODIESTERASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 26)

Asymmetric Unit (3, 26)
No.NameCountTypeFull Name
1EDO17Ligand/Ion1,2-ETHANEDIOL
2MG4Ligand/IonMAGNESIUM ION
3MLI5Ligand/IonMALONATE ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2MG-1Ligand/IonMAGNESIUM ION
3MLI1Ligand/IonMALONATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2MG-1Ligand/IonMAGNESIUM ION
3MLI2Ligand/IonMALONATE ION
Biological Unit 3 (2, 5)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2MG-1Ligand/IonMAGNESIUM ION
3MLI1Ligand/IonMALONATE ION
Biological Unit 4 (2, 4)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2MG-1Ligand/IonMAGNESIUM ION
3MLI1Ligand/IonMALONATE ION

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:205 , GLN A:206BINDING SITE FOR RESIDUE EDO A 401
02AC2SOFTWAREASP A:128 , GLU A:158 , LYS A:311 , MLI A:403 , HOH A:501 , HOH A:520 , HOH A:554BINDING SITE FOR RESIDUE MG A 402
03AC3SOFTWAREASN A:126 , GLU A:158 , HIS A:232 , SER A:235 , ASN A:273 , MG A:402 , HOH A:509 , HOH A:619 , HOH A:632BINDING SITE FOR RESIDUE MLI A 403
04AC4SOFTWAREASN A:150 , LEU A:173 , SER A:192 , HOH A:533 , HOH A:538BINDING SITE FOR RESIDUE EDO A 404
05AC5SOFTWAREARG A:237 , ARG A:275 , ARG C:344BINDING SITE FOR RESIDUE EDO A 405
06AC6SOFTWAREASP A:114BINDING SITE FOR RESIDUE EDO A 406
07AC7SOFTWAREHIS B:204 , PHE B:205 , GLN B:206BINDING SITE FOR RESIDUE EDO B 401
08AC8SOFTWAREGLU D:113 , ASP D:114 , LEU D:115BINDING SITE FOR RESIDUE EDO B 402
09AC9SOFTWAREASP B:128 , GLU B:158 , MLI B:404 , HOH B:505 , HOH B:537 , HOH B:614BINDING SITE FOR RESIDUE MG B 403
10BC1SOFTWAREASN B:126 , GLU B:158 , HIS B:232 , SER B:235 , ASP B:271 , ASN B:273 , MG B:403 , HOH B:512 , HOH B:517 , HOH B:614BINDING SITE FOR RESIDUE MLI B 404
11BC2SOFTWAREGLY B:285 , TRP B:326 , SER B:327 , GLY B:328 , LEU B:330 , HOH B:647BINDING SITE FOR RESIDUE EDO B 405
12BC3SOFTWAREASN B:150 , PRO B:151 , ASP B:152 , SER B:192 , HOH B:538 , HOH B:635 , HOH B:637 , HOH B:638BINDING SITE FOR RESIDUE MLI B 406
13BC4SOFTWAREPHE B:314 , HOH B:601BINDING SITE FOR RESIDUE EDO B 407
14BC5SOFTWAREGLN B:341 , ARG B:342 , HOH B:557 , LEU C:130 , ASP C:131 , GLY C:132BINDING SITE FOR RESIDUE EDO B 408
15BC6SOFTWAREHIS B:144BINDING SITE FOR RESIDUE EDO B 409
16BC7SOFTWAREASP C:128 , GLU C:158 , MLI C:402 , HOH C:506 , HOH C:546 , HOH C:647BINDING SITE FOR RESIDUE MG C 401
17BC8SOFTWAREASN C:126 , GLU C:158 , HIS C:232 , SER C:235 , ASN C:273 , MG C:401 , HOH C:521 , HOH C:528 , HOH C:647BINDING SITE FOR RESIDUE MLI C 402
18BC9SOFTWAREPHE C:205 , GLN C:206BINDING SITE FOR RESIDUE EDO C 403
19CC1SOFTWARELYS A:181 , PHE C:118 , GLU C:119BINDING SITE FOR RESIDUE EDO C 404
20CC2SOFTWAREASP A:168 , HOH A:546 , GLU C:119 , ASP C:152 , HOH C:569 , HOH C:646BINDING SITE FOR RESIDUE EDO C 405
21CC3SOFTWAREASN C:150 , PRO C:151 , ASP C:152 , LEU C:173 , HOH C:501 , HOH C:543BINDING SITE FOR RESIDUE EDO C 406
22CC4SOFTWAREASP D:128 , GLU D:158 , MLI D:402 , HOH D:529 , HOH D:589 , HOH D:617BINDING SITE FOR RESIDUE MG D 401
23CC5SOFTWAREASN D:126 , GLU D:158 , HIS D:232 , SER D:235 , ASP D:271 , ASN D:273 , MG D:401 , EDO D:404 , HOH D:514 , HOH D:515 , HOH D:589 , HOH D:626BINDING SITE FOR RESIDUE MLI D 402
24CC6SOFTWAREPHE D:205 , GLN D:206 , HOH D:556BINDING SITE FOR RESIDUE EDO D 403
25CC7SOFTWARETHR D:236 , ASN D:273 , ARG D:275 , PHE D:321 , MLI D:402 , HOH D:626BINDING SITE FOR RESIDUE EDO D 404
26CC8SOFTWARESER D:121 , VAL D:149 , ASN D:150 , ASP D:152 , HOH D:588BINDING SITE FOR RESIDUE EDO D 405

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FVA)

(-) 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:249
                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhh.eeeee.......eeeeeee...eeeeeeeee........eeeeeeeee..eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhh.......eehhhhh..hhhhh..ee.............ee..eeeeee....eeeeeee................eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fva A 114 DLKGFEVSVMSWNIDGLDGRSLLTRMKAVAHIVKNVNPDILFLQEVVDRDLAPIDKLQSLYKIYYSNKGCQYYTAILVSKMFDVEKHDVIHFQNSGMYRTLQILEGSIGGLKVFLLNTHLESTREHRPQRCAQFGFCMDKVREIIAQNPGALVFFGGDLNLRDEEVSRVPDGVKDAWEAAGSDNKTKFTWDTFKNDNKQGFHGAKMRFDRLYWSGPLDKVKFTLEGRQRIRSCLCFPSDHWAINATFFA 362
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353         


Chain B from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhh.eeeee.......eeeeeee...eeeeeeeee........eeeeeeeee..eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhh.......eehhhhh..hhhhh..ee.............ee..eeeeee....eeeeeee................eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fva B 113 EDLKGFEVSVMSWNIDGLDGRSLLTRMKAVAHIVKNVNPDILFLQEVVDRDLAPIDKLQSLYKIYYSNKGCQYYTAILVSKMFDVEKHDVIHFQNSGMYRTLQILEGSIGGLKVFLLNTHLESTREHRPQRCAQFGFCMDKVREIIAQNPGALVFFGGDLNLRDEEVSRVPDGVKDAWEAAGSDNKTKFTWDTFKNDNKQGFHGAKMRFDRLYWSGPLDKVKFTLEGRQRIRSCLCFPSDHWAINATFFA 362
                                   122       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:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhh.eeeee.......eeeeeee...eeeeeeeee........eeeeeeeee..eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhh.......eehhhhh..hhhhh..ee.............ee..eeeeee....eeeeeee................eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fva C 112 AEDLKGFEVSVMSWNIDGLDGRSLLTRMKAVAHIVKNVNPDILFLQEVVDRDLAPIDKLQSLYKIYYSNKGCQYYTAILVSKMFDVEKHDVIHFQNSGMYRTLQILEGSIGGLKVFLLNTHLESTREHRPQRCAQFGFCMDKVREIIAQNPGALVFFGGDLNLRDEEVSRVPDGVKDAWEAAGSDNKTKFTWDTFKNDNKQGFHGAKMRFDRLYWSGPLDKVKFTLEGRQRIRSCLCFPSDHWAINATFFA 362
                                   121       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 D from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhh.eeeee.......eeeeeee...eeeeeeeee........eeeeeeeee..eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhh.......eehhhhh..hhhhh..ee...........ee..eeeeee....eeeeeee................eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fva D 113 EDLKGFEVSVMSWNIDGLDGRSLLTRMKAVAHIVKNVNPDILFLQEVVDRDLAPIDKLQSLYKIYYSNKGCQYYTAILVSKMFDVEKHDVIHFQNSGMYRTLQILEGSIGGLKVFLLNTHLESTREHRPQRCAQFGFCMDKVREIIAQNPGALVFFGGDLNLRDEEVSRVPDGVKDAWEAAGSDNKTKFTWDTFKNDNKQGGAKMRFDRLYWSGPLDKVKFTLEGRQRIRSCLCFPSDHWAINATFFA 362
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312||     324       334       344       354        
                                                                                                                                                                                                                                  313|                                              
                                                                                                                                                                                                                                   316
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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 4FVA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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        TYDP2_CAEEL | Q9XWG3: 4f1i 4gew

(-) Related Entries Specified in the PDB File

4f1h 4f1i 4fpv 4gew