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(-) Description

Title :  STRUCTURE OF THE ENZYME-PRODUCT COMPLEX RESULTING FROM TDG ACTION ON A GCAC MISMATCH
 
Authors :  E. Pozharski, S. S. Malik, A. C. Drohat
Date :  30 Jul 15  (Deposition) - 16 Sep 15  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Protein-Dna Complex, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. S. Malik, K. M. Varney, E. Pozharski, A. C. Drohat
Characterizing The Enzyme-Product Complexes Of Thymine Dna Glycosylase Using Crystallography And Nmr
Nucleic Acids Res. 2015
PubMed: search

(-) Compounds

Molecule 1 - G/T MISMATCH-SPECIFIC THYMINE DNA GLYCOSYLASE
    Chains: A
    EC Number: 3.2.2.29
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: CORE DOMAIN
    Gene: TDG
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: THYMINE-DNA GLYCOSYLASE,HTDG
 
Molecule 2 - DNA (28-MER)
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (28-MER)
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ACD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2ORP1Mod. Nucleotide2-DEOXY-5-PHOSPHONO-RIBOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:138 , ILE A:139 , ASN A:140 , TYR A:152 , ASN A:191 , HOH A:505 , HOH A:509 , HOH A:540 , ORP D:17binding site for residue ACY A 401
2AC2SOFTWAREASN A:140 , PRO A:141 , ASN A:157 , THR A:197 , SER A:200 , SER A:271 , SER A:273 , ALA A:274 , ARG A:275 , CYS A:276 , ALA A:277 , GLN A:278 , ACY A:401 , DA C:10 , DC C:11 , DG C:12 , DT C:13 , DG C:14 , DC D:15 , DT D:19 , HOH D:102 , HOH D:124binding site for Poly-Saccharide residues DA D 16 through DG D 18

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CYS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5CYS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CYS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CYS)

(-) Exons   (0, 0)

(no "Exon" information available for 5CYS)

(-) 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:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh.............eeeee...hhhhhhhh........hhhhhhhhh.......hhhhhhhhhhhhheeeee............hhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh........eeeeee......eeeee...............hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cys A 109 ASFNGVSEAELLTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIERN 305
                                   118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       


Chain C from PDB  Type:DNA  Length:28
                                                            
                 5cys C   1 CAGCTCTGTACGTGAGCGATGGACAGCT  28
                                    10        20        


Chain D from PDB  Type:DNA  Length:28
                                                            
                 5cys D   1 AGCTGTCCATCGCTCAxGTACAGAGCTG  28
                                    10      | 20        
                                           17-ORP
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  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 5CYS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CYS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CYS)

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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  TDG_HUMAN | Q13569
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  3.2.2.29
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 Related Entries

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

UniProtKB/Swiss-Prot
        TDG_HUMAN | Q13569: 1wyw 2d07 2rba 3ufj 3uo7 3uob 4fnc 4jgc 4xeg 4z3a 4z47 4z7b 4z7z 5ff8 5hf7 5jxy 5t2w

(-) Related Entries Specified in the PDB File

4xeg 4z3a 4z47 4z7b 4z7z